Dissertations / Theses on the topic 'Genotype'

L'interaction genotype*milieu observee sur le rendement a ete expliquee sur un reseau multilocal de ble tendre d'hiver a l'aide de genotypes revelateurs. Ces genotypes, revelateurs de facteurs limitants du milieu, sont specifiquement choisis sur la base de leur comportement particulier vis a vis d'un ou plusieurs facteurs du milieu. Le corps principal de la these se compose de quatre articles. Le principal resultat de la revue bibliographique reside dans la comparaison de trois modelisations statistiques, regression conjointe, modele ammi et regression factorielle, a l'aide d'exemples issus de nombreuses especes. Cet article a permis de mettre en evidence que peu de demarches sont a la fois d'ordre statistique et agro-physiologique, d'ou l'interet de la these. Le deuxieme article est consacre a la caracterisation des milieux a l'aide de quatre genotypes revelateurs. Deux variables synthetiques ont ete analysees : la deviation du nombre de grains par rapport a une valeur de reference, qui permet de porter un diagnostic sur ce qui s'est passe jusqu'a la floraison, et la reduction du poids de mille grains a une valeur de reference, qui permet de juger des conditions de remplissage. Les valeurs de reference ont ete determinees a partir de courbes enveloppes. Les derniers articles ont aborde l'analyse de l'interaction observee sur douze varietes ou les covariables du milieu, indicateurs usuels de facteurs limitants du rendement tels les indicateurs physiques ou biologiques, ou les deviations de composantes mesurees sur les genotypes revelateurs, ont ete integrees dans des modeles de regressions factorielles lineaire et bilineaire. En outre, des resultats et des discussions ont complete les articles initiaux.

A variety of modern software packages are available for genotype imputation relying on advanced concepts such as pre-phasing of the target dataset or utilization of admixed reference panels. In this study, we performed a comprehensive evaluation of the accuracy of modern imputation methods on the basis of the publicly available POPRES samples. Good quality genotypes were masked and re-imputed by different imputation frameworks: namely MaCH, IMPUTE2, MaCH-Minimac, SHAPEIT-IMPUTE2 and MaCH-Admix. Results were compared to evaluate the relative merit of pre-phasing and the usage of admixed references. We showed that the pre-phasing framework SHAPEIT-IMPUTE2 can overestimate the certainty of genotype distributions resulting in the lowest percentage of correctly imputed genotypes in our case. MaCH-Minimac performed better than SHAPEIT-IMPUTE2. Pre-phasing always reduced imputation accuracy. IMPUTE2 and MaCH-Admix, both relying on admixed-reference panels, showed comparable results. MaCH showed superior results if well-matched references were available (Nei’s GST ≤ 0.010). For small to medium datasets, frameworks using genetically closest reference panel are recommended if the genetic distance between target and reference data set is small. Our results are valid for small to medium data sets. As shown on a larger data set of population based German samples, the disadvantage of pre-phasing decreases for larger sample sizes.

Thesis (Master of Architecture)--University of Cincinnati, 2007.
Title from electronic theses title page (viewed July 16, 2007). Includes abstract. Keywords: architecture; typology; therapeutic; riding stable Includes bibliographic references.

The porphyrias are a group of disorder resulting from defects in the haem biosynthesis pathway. The majority of defects are genetic in origin. The clinical penetrance of porphyria is variable and cannot be explained by environmental factors alone. It is therefore likely that genetic modifiers are present to influence the phenotypic outcome of the disease. In the first part of this study, variants in ABCB6, a member of the ATP-Binding Cassette transporter, were detected in a high proportion (62.5%) of severely affected porphyria patients. In vitro functional studies revealed that these ABCB6 variants either affect dimer formation (p.Arg276Trp, p.Thr521Ser, p.Gly588Ser and p.Ala681Thr), or has decreased ATPase activity (p.Ala492Thr). In a double knock out mouse model deficiency in Fech (Fechm1Pas) and Abcb6 showed a more severe phenotype compared to Fechm1Pas-only mice. The results support that ABCB6 acts as a genetic modifier for porphyria patients. In the second part of this study, detailed study on a patient with fatal liver failure secondary to erythropoietic protoporphyria (EPP) revealed an atypical low expression FECH allele and a maternally inherited FECH p.Phe260Leu mutation giving rise to the EPP. Exome sequencing of this EPP patient and her parents revealed multiple functional variants and a novel 0.79Mb duplication, all involving genes in the bile secretion pathway. These variants affect both the basolateral re-uptake and canalicular secretion of bile acids as well as their constitution. In EPP, the excessive haem intermediate protoporphyrin IX is excreted in bile. The results here suggest that genetic variants in the bile secretion pathway may contribute to the risk of liver failure in EPP patients.

Introducció. La hidrosadenitis supurativa (HS) és una malaltia crònica, inflamatòria de la unitat pilosebàcia. Es caracteritza per la formació de nòduls, abscessos i fístules en zones riques en glàndules apocrines. L’etiopatogènia és multifactorial i es relaciona amb múltiples comorbiditats. L’expressió clínica és diferent interindividualment i intraindividualment a mesura que la malaltia progressa. S’ha proposat que diverses vies patogèniques serien les responsables de l’expressió fenotípica variada i s’han descrit algunes classificacions fenotípiques basades en dades clíniques i epidemiològiques. Objectius. L’objectiu principal fou classificar als pacients de la nostre cohort en dos clústers que es poden interpretar com a endotips de la malatia. Els objectius secundaris foren: determinar si els pacients amb afectació del clatell i les pacients amb afectació de la vulva pertanyien a un fenotip atípic; descriure el subgrup de pacients amb Malaltia de Dowling-Degos (MDD) i HS i, per últim, analitzar el perfil antropomètric d’un grup de malalts amb HS en comparació als malalts amb psoriasi i a un grup control. Material i mètodes. S’analitzà la cohort de pacients tractats a les consultes monogràfiques de HS. Per a l’estudi de la MDD també s’inclogueren pacients de l’Hospital General de Alicante. Les dades que es recolliren dels pacients foren els antecedents familiars, personals i epidemiològics; les característiques clíniques; les mesures antropomètriques i els tractaments. En 103 pacients, també s’analitzaren paràmetres analítics (hemograma, vitamina D, insulina, HLA B27, proteïnograma, funció hepàtica i renal), inflamatoris (VSG, PCR, interleuquines 10,1,6 i 17) i mutacions de la via gamma secretasa (APH1A, APH1B, MEFV, NCSTN, PSEN1, PSEN2, PSENEN, PSTPIP1). Resultats. S’obtingueren dos grups. El grup (C1) o atípic estava format per pacients no obesos, la majoria homes, amb un debut precoç, alteracions de la via gamma secretasa, increment de IL-10 i lesions en la part posterior del tronc tipus acne conglobata i fol·liculitis cicatricial. El segon grup (C2) es caracteritzava per incloure pacients obesos, amb un debut més tardà, amb un increment de la PCR, ILs-1, 6 i 17; per la formació d’abscessos i de lesions en la part anterior del cos. El subgrup de pacients amb afectació del clatell es podia incloure dins el C1, ja que presentaven més gravetat i la majoria eren homes prims. Les malaltes amb afectació de la vulva, també presentaven un fenotip atípic amb predomini de lesions fol·liculars i cicatricials, un IMC inferior, una major gravetat, però excepcionalment un debut més tardà. D’altra banda, els pacients afectes de MDD presentaven un debut més precoç i un patró clínic compatible amb el grup C1, però per contra, un 53% dels malalts tenien sobrepès i pràcticament de forma constant lesions axil·lars i engonals (característic del grup C2). Quan es comparava l’IMC i el percentatge de greix corporal entre pacients amb HS, psoriasi i un grup control, s’observa que el percentatge de greix corporal era superior en els pacients amb HS en comparació al grup control (P=0,02), però no s’observarà cap relació amb la gravetat. En fases inicials de la malaltia, el pilar terapèutic dels pacients del grup C1 serien els fàrmacs amb acció sobre la unitat fol·licular (acitretina, gluconat de zinc, sulfona, colquicina, antiandrògens), mentre que als del grup C2, serien els antibiòtics. Conclusions. Existeixen dos clústers interpretables com a endotips: el C2 o típic i el C1 o atípic, on s’inclouen els malalts amb afectació del clatell, la vulva i els malalts amb MDD. No hi ha cap tractament curatiu per se i els equips multidisciplinars per al maneig integratiu del malalt són indispensables.
Introducción. La hidrosadenitis supurativa (HS) es una enfermedad crónica, inflamatoria de la unidad pilosebácea. Se caracteriza por la formación de nódulos, abscesos y fístulas en zonas ricas en glándulas apocrinas. La etiopatogenia es multifactorial y se relaciona con múltiples comorbilidades. La expresión clínica es diferente interindividualmente y intraindividualment a medida que la enfermedad progresa. Se ha propuesto que diversas vías patogénicas serían las responsables de la expresión fenotípica variada y se han descrito algunas clasificaciones fenotípicas basadas en datos clínicos y epidemiológicos. Objetivos. El objetivo principal fue clasificar a los pacientes de nuestra cohorte en dos clústeres que se pueden interpretar como endotipos de la enfermedad. Los objetivos secundarios fueron: determinar si los pacientes con afectación de la nuca y las pacientes con afectación de la vulva pertenecían a un fenotipo atípico; describir el subgrupo de pacientes con Enfermedad de Dowling-Degos (MDD) y HS y, por último, analizar el perfil antropométrico de un grupo de enfermos con HS en comparación a los enfermos con psoriasis y a un grupo control. Material y métodos. Se analizó la cohorte de pacientes tratados en las consultas monográficas de HS. Para el estudio de la MDD también se incluyeron pacientes del Hospital General de Alicante. Los datos que se recogieron de los pacientes fueron los antecedentes familiares, personales y epidemiológicos; las características clínicas; las medidas antropométricas y los tratamientos. En 103 pacientes, también se analizaron parámetros analíticos (hemograma, vitamina D, insulina, HLA B27, proteinograma, función hepática y renal), inflamatorios (VSG, PCR, interleucinas 10,1,6 y 17) y mutaciones de la vía gama secretasa (APH1A, APH1B, MEFV, NCSTN, PSEN1, PSEN2, psenes, PSTPIP1). Resultados. Se obtuvieron dos grupos. El grupo (C1) o atípico estaba formado por pacientes no obesos, la mayoría hombres, con un debut precoz, alteraciones de la vía gama secretasa, incremento de IL-10 y lesiones en la parte posterior del tronco tipo acné conglobata y foliculitis cicatricial. El segundo grupo (C2) se caracterizaba por incluir pacientes obesos, con un debut más tardío, con un incremento de la PCR, ILs-1, 6 y 17; por la formación de abscesos y de lesiones en la parte anterior del cuerpo. El subgrupo de pacientes con afectación de la nuca se podía incluir en el C1, ya que presentaban mayor gravedad y la mayoría eran hombres delgados. Las enfermas con afectación de la vulva, también presentaban un fenotipo atípico con predominio de lesiones foliculares y cicatriciales, un IMC inferior, una mayor gravedad, pero excepcionalmente un debut más tardío. Por otra parte, los pacientes afectos de MDD presentaban un debut más precoz y un patrón clínico compatible con el grupo C1, pero por el contrario, un 53% de los enfermos tenían sobrepeso y prácticamente de forma constante lesiones axilares e ingles (característico del grupo C2). Cuando se comparaba el IMC y el porcentaje de grasa corporal entre pacientes con HS, psoriasis y un grupo control, se observa que el porcentaje de grasa corporal era superior en los pacientes con HS en comparación al grupo control (P = 0,02 ), pero no se observará ninguna relación con la gravedad. En fases iniciales de la enfermedad, el pilar terapéutico de los pacientes del grupo C1 serían los fármacos con acción sobre la unidad folicular (acitretina, gluconato de zinc, sulfona, colchicina, antiandrógenos), mientras que los del grupo C2, serían los antibióticos . Conclusiones. Existen dos clústeres interpretables como endotipos: el C2 o típico y el C1 o atípico, donde se incluyen los enfermos con afectación de la nuca, la vulva y los enfermos con MDD. No hay ningún tratamiento curativo para y los equipos multidisciplinares para el manejo integral del enfermo son indispensables.
Introduction. Hidrosadenitis suppurativa (HS) is a chronic, inflammatory disease of the pilosebaceous unit. It is characterized by the formation of nodules, abscesses and fistulas in areas rich in apocrine glands. The etiopathogenesis is multifactorial and is related to multiple comorbidities. Clinical expression differs interindividually and intraindividually as the disease progresses. It has been proposed that several pathogenic pathways would be responsible for the varied phenotypic expression. Some phenotypic classifications based on clinical and epidemiological data have been described. Objectives. The main objective was to classify the patients in our cohort into two clústers that could be regarded as endotypes. The secondary endpoints were: to determine whether patients with cervical involvement and patients with vulvar involvement belonged to an atypical phenotype of the disease; describe the subgroup of patients with Dowling-Degos Disease (MDD) and for last, to analyze the anthropometric profile of a group of patients with HS compared to patients with psoriasis and a control group. Material and methods. The cohort of patients treated in the monographic consultations of HS was analyzed. For the study of MDD, five patients from the General Hospital of Alicante were also gathered. The data collected from patients were: family, personal and epidemiological history; clinical features; anthropometric measurements and treatments. In 103 patients, analytical parameters (hemogram, vitamin D, insulin, HLA B27, proteinogram, liver and kidney function), inflammatory (ESR, PCR, interleukins 10, 1, 6, and 17), and mutations in the gamma secretase pathway were also analyzed (APH1A, APH1B, MEFV, NCSTN, PSEN1, PSEN2, PSENEN, PSTPIP1). Results. Two groups were obtained. The group (C1) or atypical was made up of non-obese patients, mostly men, with an early onset, alterations of the gamma secretase pathway, increased IL-10 and lesions in the back of the trunk like acne conglobata and cicatricial follyculitis. The second group (C2) was characterized by including obese patients, with a later onset, with an increase in PCR, ILs-1, 6, and 17 and by the formation of abscesses and lesions in the anterior part of the body. The subgroup of patients with neck involvement could be included within C1, as they presented more severity and most were thin men. Patients with vulvar involvement also had an atypical phenotype with a predominance of follicular and scarring lesions, a lower BMI, a higher severity, but exceptionally a later onset. In contrast, patients with MDD had an earlier onset and a clinical pattern compatible with the C1 group, but in contrast, 53% of them were overweight and most of them had either axillary or inguinal involvement (typical of C2). When comparing BMI and body fat percentage between patients with HS, psoriasis and a control group, it was observed that the percentage of body fat was higher in patients with HS compared to the control group (P = 0.02), but no relation to severity. In the early stages of the disease, the mainstay of treatment for patients in group C1 are those drugs that act on the follicular unit (acitretin, zinc gluconate, sulfone, colchicine, antiandrogens), while for those patients in group C2, antibiotics. Conclusions. There are two clústers/endotypes: C2 or typical and C1 or atypical, which includes patients with neck, vulva and MDD involvement. There is no curative treatment per se and multidisciplinary teams that carry out an integrative patient management are mandatory.

Meningioma and glioma are the most common primary brain tumors, but their etiologies are largely unknown. Although meningioma is usually benign, their intracranial location can lead to lethal consequences, and despite progress in surgery, radiotherapy, and chemotherapy the prognosis for patients with glioma remains poor. The only well-established environmental risk factor for meningioma and glioma is ionizing radiation. Evidence for inherited predisposition to meningioma and glioma is provided by a number of rare inherited syndromes where collectively these diseases account for only a small proportion of the twofold increased risk of brain tumors seen in first-degree relatives for meningioma and glioma patients. It is very possible that much of the excess familial risk is a consequence of co-inheritance of multiple low-risk genetic variations. With this in mind, the aims of the studies in this thesis were to discover genetic risk variants influencing the probability of acquiring the disease and to identify the association between risk variants on the tumor phenotype. To identify genetic variants influencing meningioma risk, a comprehensive tagging of the selected genes in a case-control study was performed. We identified nine risk variants in EGF, ERBB2, and LRIG2 genes. However, these findings could not be confirmed in another larger independent dataset. In addition, the study identified a correlation between LRIG2 protein expression and ER status when analyzed with different parameters. In a separate study with a larger sample of meningioma patients, the same correlation between LRIG2 and ER status was observed. To explore the potential association between reported germline risk variants and somatic genetic events, matched tumor and blood samples from glioma patients were analyzed by SNP array. The results identified correlations between EGFR gene variants and somatic aberrations within the EGFR locus and CDKN2A/B locus. To further study the relationship between germline risk variants and tumor phenotype, the same patient material was used and analyzed by three different techniques: SNP array, IHC, and FISH. The results revealed EGFR risk variants effecting copy number variation of the EGFR gene and the expression of the IDH1 and p53. Further comparison between different techniques such as SNP array and FISH analysis revealed the difficulty in achieving consistent results with different techniques. To summarize, the glioma studies show a link between genotype and phenotype where genetic risk variants in the EGFR gene were found to be associated with specific somatic aberrations. These associations are biologically interesting because EGFR is involved in multiple cellular processes. Additional studies of the direct functional role of these observations need to be conducted to elucidate the molecular mechanisms underlying the identified association between germline gene variants and somatic aberrations. For the meningioma studies, no significant risk variants influencing the disease were found but a correlation between LRIG2 and ER status was observed. This result suggests a potential role for the LRIG protein in the pathogenesis of meningioma, but more studies are needed to confirm this hypothesizes.

Cancer research foundation in northern Sweden and Lions cancer research foundation at Umeå university

The interaction effects of genotype and nutrition on the performance of sows during lactation is still poorly understood; this series of experiments explored the factors contributing to breed differences in lactational performance and the development of appropriate feeding strategies. Two extreme types of sow were used in these experiments; lean pure-bred White sows (W: Large White and Landrace) and a prolific but fatter Meishan synthetic damline (M: 50% Meishan genes). M sows had higher numbers of piglets, a different feed intake curve and produced more milk with a higher fat content compared to W breed types. Their response to dietary protein was different for the two breeds; the Meishan sows, with higher initial levels of body fat reserves, used the extra protein to increase milk production. The White sows did not partition the extra protein into milk but used it to conserve their own maternal body reserves and improved their weaning to conception interval. The breed differences in sows performance were found not to be solely due to differences in litter size or piglet genotype or maternal body fat reserves. M sows showed better maternal behaviour with lower activity and shorter suckling intervals. It can be concluded from these experiments that Meishan synthetic sows are inherently better mothers, and the way in which sows of different breed types partition feed nutrients during lactation is very different. A dietary lysine concentration of 9 g/kg (giving daily intakes of 53-61 g/day at 98-111 MJ DE/day) optimised lactational and rebreeding performance in both breed types.

This thesis explores genotype-phenotype relations in lupus nephritis. Over the past decade, advances in genetic research have improved our understanding of the genes that contribute to lupus susceptibility. However a clear understanding of how these genetic factors interact with the immune system to produce disease in a given patient or group of patients with SLE is difficult to define at this time. Recent monogenic causes of SLE have provided valuable insights into lupus pathogenesis. A comprehensive clinical characterisation of 164 biopsy proven lupus nephritis patients was undertaken in the initial phase of this research. 27% of patients recruited were of juvenile onset, as defined by diagnosis of nephritis before 18 years of age. Non-European lupus nephritis patients had a younger age of onset and higher rate of progression to end-stage renal disease. Sixteen individuals had a first degree family history of lupus nephritis including five sibling pairs. Familial clustering of nephritis was associated with juvenile onset disease and a more severe clinical phenotype. The entire cohort was genotyped by ImmunoChip for known lupus susceptibility polymorphisms. Associations with lupus nephritis were found in polymorphisms in the HLA region, IRF5, ITGAM, STAT4, TNFAIP3, TNFSF4 and ETS1. Whole Exome Sequencing of familial lupus nephritis cases identified a large number of potential candidates for functional investigation. A promising short list of candidates was created using pedigree information, focusing on variants predicted to be damaging and by incorporating prior knowledge of the biologic pathways implicated in lupus. Candidates under consideration for functional testing include genes involved in activation of Ras pathways, genes involved in the antioxidant defence system, variants in ubiquitination pathways, mutations in serine/threonine protein kinases and genes involved in toll-like receptor and type I interferon signalling pathways.

Among the most fundamental features shared by all organisms is the mapping of information encoded in genotypes (genetic material) to generate phenotypes (biological structures, functions, and traits). Hence, elucidating the structure of genotype-phenotype (GP) maps is important for understanding evolution and biology. While it is known that often GP maps are highly degenerate with many different genotypes adopting the same phenotype, the distribution of genotypes over phenotypes is less well studied. In this thesis we investigate the question of the distribution of genotypes over phenotypes, or put differently the distribution of neutral set sizes (NSS), where a neutral set is the collection of all genotypes in a GP map which map to the same phenotype. We focus on examining phenotypic bias in GP maps, where some phenotypes have disproportionally large NSS as compared to others. We find phenotypic bias to be ubiquitous in the broad range of GP maps that we analyse, from the genetic code up to molecular RNA to a model of neuronal connections, and hence we hypothesise bias to be a common property of GP maps. Further, we also consider the implications that this bias has for evolutionary outcomes, and we argue that bias is a significant influencing factor in determining evolutionary outcomes. Finally, we propose a method to predict a phenotype's NNS via estimating the phenotype's structural complexity, without using detailed knowledge about the specifics of the relevant GP map. We achieve this via a novel application of algorithmic information theory and especially Levin's coding theorem.

Stage II/III CRCs are currently treated by surgery, then stage III and stage II patients exhibiting high-risk pathological features undergo a course of 5-FUbased adjuvant chemotherapy, often with oxaliplatin added. Improved characterisation of stage 11/111 tumours is required in order to improve their treatment and to ensure that drugs are only given to patients where there is evidence of a likely response. This will reduce the unnecessary and costly overtreatment of these patients, as well as the associated unpleasant side effects. Pyrosequencing, immunohistochemistry, FISH, and next-generation sequencing were used in order to assess a number of molecular markers of high-risk stage 11 CRCs in two cohorts. Of the markers tested, only mutation in KRAS was prognostic in stage 11/11I CRC (HR = 1.4). Mutation of BRAF, NRAS, PIK3CA and overexpression/amplification of HER-2 were not prognostic or predictive of response to 5-FU chemotherapy in the QUASAR-1 trial. TOP2A was coamplified with HER-2 in 28% cases. Copy number profiles produced from this cohort showed the differences between dMMR and pMMR, and the effect of high stromal content on CNV. Cases from the QUASAR-1 fit into one of three groups regarding CNV which need further characterisation and their relationship to prognosis needs to be established. KRAS mutation is a prognostic marker in stage 11/11I disease and could be tested for routinely. Importantly none of the other markers tested predicted a worse outcome with 5-FU-based chemotherapy. TOP2A is frequently coamplified with HER-2 suggesting that a subset of these cases may respond to anthracycline therapy.

Accessibility of high-throughput genotyping technology makes possible genome-wide association studies for common complex diseases. When dealing with common diseases, it is necessary to search and analyze multiple independent causes resulted from interactions of multiple genes scattered over the entire genome. The optimization formulations for searching disease-associated risk/resistant factors and predicting disease susceptibility for given case-control study have been introduced. Several discrete methods for disease association search exploiting greedy strategy and topological properties of case-control studies have been developed. New disease susceptibility prediction methods based on the developed search methods have been validated on datasets from case-control studies for several common diseases. Our experiments compare favorably the proposed algorithms with the existing association search and susceptibility prediction methods.

This study focuses how the MLR-tagging for statistical covering, i.e. either maximizing average R2 for certain number of requested tags or minimizing number of tags such that for any non-tag SNP there exists a highly correlated (squared correlation R2 > 0.8) tag SNP. We compare with tagger, a software for selecting tags in hapMap project. MLR-tagging needs less number of tags than tagger in all 6 cases of the given test sets except 2. Meanwhile, Biologists can detect or collect data only from a small set. So, this will bring a problem for scientists that the estimates accuracy of tag SNPs when constructing the complete human haplotype map. This study investigates how the MLR-tagging for statistically coverage performs under unbias study. The experiment results shows MLR-tagging still select small amount of SNPs very well even without observing the entire SNP in the sample.

Single nucleotide polymorphisms (SNPs) are DNA sequence variations, occurring when a single nucleotide –A, T, C or G – is altered. Arguably, SNPs account for more than 90% of human genetic variation. Dr. Tebbutt's laboratory has developed a highly redundant SNP genotyping assay consisting of multiple probes with signals from multiple channels for a single SNP, based on arrayed primer extension (APEX). The strength of this platform is its unique redundancy having multiple probes for a single SNP. Using this microarray platform, we have developed fully-automated genotype calling algorithms based on linear models for individual probe signals and using dynamic variable selection at the prediction level. The algorithms combine separate analyses based on the multiple probe sets to give a final confidence score for each candidate genotypes. Our proposed classification model achieved an accuracy level of >99.4% with 100% call rate for the SNP genotype data which is comparable with existing genotyping technologies. We discussed the appropriateness of the proposed model related to other existing high-throughput genotype calling algorithms. In this thesis we have explored three new ideas for classification with high dimensional data: (1) ensembles of various sets of predictors with built-in dynamic property; (2) robust classification at the prediction level; and (3) a proper confidence measure for dealing with failed predictor(s). We found that a mixture model for classification provides robustness against outlying values of the explanatory variables. Furthermore, the algorithm chooses among different sets of explanatory variables in a dynamic way, prediction by prediction. We analyzed several data sets, including real and simulated samples to illustrate these features. Our model-based genotype calling algorithm captures the redundancy in the system considering all the underlying probe features of a particular SNP, automatically down-weighting any ‘bad data’ corresponding to image artifacts on the microarray slide or failure of a specific chemistry. Though motivated by this genotyping application, the proposed methodology would apply to other classification problems where the explanatory variables fall naturally into groups or outliers in the explanatory variables require variable selection at the prediction stage for robustness.

Genotype-by-environment interactions (G x Es) describe genetic variation for phenotypic plasticity, such that the relative performance of genotypes varies across environments. These interactions have been studied in the context of natural selection for decades, but research interest in the evolutionary consequences of G x Es in sexual traits is more recent. Theory suggests that G x Es in sexual traits could be of fundamental importance to the operation of sexual selection across heterogeneous environments, but empirical research lags behind the theory. In this thesis, I review the current literature on the role of G x Es in sexual selection and identify areas for further research. Using cuticular hydrocarbons (CHCs) in the fruit fly Drosophila simulans as a model system for sexual selection, I examine G x Es in trait expression and quantify the effect of these G x Es in terms of sexual signal reliability and the coevolution of male and female sexual traits. To do so, I use a combination of quantitative genetics and laboratory environmental manipulations. First, I demonstrate that male CHC profile is subject to sexual selection through female mate choice and find some variation in patterns of mate choice across diets and temperatures (Chapter 3). Next, I identify G x Es in male and female CHC expression across diets and temperatures, although G x Es in male CHC profile across temperatures are weak (Chapter 4). I find that G x Es in male CHC expression can cause sexual signal unreliability, as predicted by theory, since male CHCs do not reliably signal heritable aspects of male attractiveness across diets and temperatures (Chapter 5). I also find G x Es in some aspects of female mate choice across temperatures (Chapter 6). In spite of the evidence for signal unreliability and variation in female mate choice across environments, I show that the overall outcome of mate choice is unaffected by G x Es, such that the same male genotypes are attractive across diets and temperatures (Chapters 5 and 6). From my results, it seems likely that females assess male attractiveness based on multiple male sexual signals, so that whilst male CHCs influence mate choice, CHC profile does not necessarily correlate well with overall male attractiveness. I discuss the implications of these results for the evolution of sexual traits and the genetic covariance between male and female sexual traits across environments. The research in this thesis highlights the importance of multivariate studies of sexual selection across environments for a more complete understanding of the evolution of sexual traits.

The phenotype inference from genotype in RNA viruses maps the viral genome/protein sequences to the molecular functions in order to understand the underlying molecular mechanisms that are responsible for the function changes. The inference is currently done through a laborious experimental process which is arguably inefficient, incomplete, and unreliable. The wealth of RNA virus sequence data in the presence of different phenotypes promotes the rise of computational approaches to aid the inference. Key residue identification and genotype-phenotype mapping function learning are two approaches to identify the critical positions out of hitchhikers and elucidate the relations among them. The existing computational approaches in this area focus on prediction accuracy, yet a number of fundamental problems have not been considered: the scalability of the data, the capability to suggest informative biological experiments, and the interpretability of the inferences. A common scenario of inference done by biologists with mutagenesis experiments usually involves a small number of available sequences, which is very likely to be inadequate for the inference in most setups. Accordingly biologists desire models that are capable of inferring from such limited data, and algorithms that are capable of suggesting new experiments when more data is needed. Another important but always been neglected property of the models is the interpretability of the mapping, since most existing models behave as ’black boxes’. To address these issues, in the thesis I design a supervised combinatorial filtering algorithm that systematically and efficiently infers the correct set of key residue positions from available labeled data. For cases where more data is needed to fully converge to an answer, I introduce an active learning algorithm to help choose the most informative experiment from a set of unlabeled candidate strains or mutagenesis experiments to minimize the expected total laboratory time or financial cost. I also propose Disjunctive Normal Form (DNF) as an appropriate assumption over the hypothesis space to learn interpretable genotype-phenotype functions. The challenges of these approaches are the computational efficiency due to the combinatorial nature of our algorithms. The solution is to explore biological plausible assumptions to constrain the solution space and efficiently find the optimal solutions under the assumptions. The algorithms were validated in two ways: 1) prediction quality in a cross-validation manner, and 2) consistency with the domain experts’ conclusions. The algorithms also suggested new discoveries that have not been discussed yet. I applied these approaches to a variety of RNA virus datasets covering the majority of interesting RNA phenotypes, including drug resistance, Antigenicity shift, Antibody neutralization and so on to demonstrate the prediction power, and suggest new discoveries of Influenza drug resistance and Antigenicity. I also prove the extension of the approaches in the area of severe acute community disease.

The global transcriptional regulator mexT, is a mutational hotspot; the sequence variants commonly seen to co-exist within the P. aeruginosa population are: drug susceptible (e.g. PAO1) and chloramphenicol and norfloxacin non-susceptible (nfxC mutant). The nfxC phenotype, selected for on chloramphenicol agar is characterised by reduced virulence. The conversion between PAO1 and nfxC phenotypes is associated with an 8-bp repeat sequence in mexT. To investigate the effects of the 8-bp repeat on the adaptive mode of survival of P. aeruginosa, isogenic mutants were generated: PA (8-bp, two copies) and PAdel (8-bp, one copy). The mutants were characterised using phenotypic microarrays (PM), motility, antibiotic susceptibility, Galleria virulence models and RNA-seq in defined media. PM revealed differences in central metabolism indicating that PAdel/PAnfxC were associated with a biological metabolic cost. Strains with the single copy of the 8-bp sequence showed reduced motility and virulence. Transcriptome analysis revealed that mexT, in PA, consists of two regulatory elements defined by an intact helix-turn-helix motif (across the repeat region) which is capable of regulating the downstream LysR region via repressor and autoregulative mechanisms. Whole genome sequencing identified regions of compensatory mutations that were associated with differences in phenotype between PAdel (genetically modified) and PAnfxC (selected). To link phenotype and genotype and to understand the metabolic effects of this mutation, a genome wide metabolic reconstruction was performed. This revealed differences in key metabolic pathways such as glycolysis, gluconeogenesis and oxidative phosphorylation. This study has shown that an 8-bp repeat in mexT is a driver of genetic diversity. Regulatory elements linked to the effect of the 8-bp sequence on antibiotic resistance, central metabolism, chemotaxis, motility and virulence have also been identified. These methods can be used to define phenotype in any pair of isogenic mutants, at the genome level, and to investigate the clinical risk of strains.

Sickle cell disease (SCD) has a complex pathophysiology initiated by the polymerisation of deoxy-sickle-haemoglobin. The single nucleotide change underpinning SCD does not account for the vast range and severity of SCD complications. This clinical heterogeneity is only partly explained by the genetic variability of fetal haemoglobin gene levels and co-inheritance of α- thalassemia. Although environmental factors also contribute to the clinical complexity of SCD, further genetic modifiers of SCD severity exist but are yet to be determined. Genetic association studies have been boosted recently not only with the advent of new genotyping tools, but also with the development of increasingly sophisticated analytical methods. New developments in phenotyping, genotyping and genotype-phenotype association approaches allow us to disentangle true genetic associations from hits due to chance. This thesis seeks to investigate biomarkers of sickle severity and to use these clinical markers in genotype-phenotype correlation studies. I have investigated three key markers of disease severity: haemolysis, frequency of acute pain episodes and mortality. Estimated median survival of 67 years in HbSS disease in our UK cohort is a significant improvement in survival compared to other recent estimates in the USA and Jamaica. I have undertaken genome-wide micro-array scanning and created an imputed genotype dataset of over 15,000,000 genetic variants. I have used these phenotype and genotype datasets to conduct genetic association studies, both genome-wide and candidate gene association studies. These analyses are based on linear mixed modelling to account for relatedness (including population stratification) within the cohort. In addition to the severity outcomes, I have also evaluated the known genetic loci for HbF and created a genetic “summary statistic” to quantify the effects of these three loci. Finally, I have also assessed the role of the erythroid regulator KLF1 in HbF levels in SCD with two laboratory-based projects.

Over the past 10 years, several synthetic biology research groups have proposed tools and domain-specific languages to help with the design of artificial DNA molecules. Community standards for exchanging data between these tools, such as the Synthetic Biology Open Language (SBOL), have been developed. It is increasingly important to be able to perform in silico simulation before the time and cost consuming wet lab realization of the constructs, which, as technology advances, also become in themselves more complex. By extending the concept of describing genetic expression as a language, we propose to model relations between genotype and phenotype using formal language theory. We use attribute grammars (AGs) to extract context-dependent information from genetic constructs and compile them into mathematical models, possibly giving clues about their phenotypes. They may be used as a backbone for biological Domain-Specific Languages (DSLs) and we developed a methodology to design these AG based DSLs. We gave examples of languages in the field of synthetic biology to model genetic regulatory networks with Ordinary Differential Equations (ODEs) based on various rate laws or with discrete boolean network models. We implemented a demonstration of these concepts in GenoCAD, a Computer Assisted Design (CAD) software for synthetic biology. GenoCAD guides users from design to simulation. Users can either design constructs with the attribute grammars provided or define their own project-specific languages. Outputting the mathematical model of a genetic construct is performed by DNA compilation based on the attribute grammar specified; the design of new languages by users necessitated the generation on-the-fly of such attribute grammar based DNA compilers. We also considered the impact of our research and its potential dual-use issues. Indeed, after the design exploration is performed in silico, the next logical step is to synthesize the designed construct's DNA molecule to build the construct in vivo. We implemented an algorithm to identify sequences of concern of any length that are specific to Select Agents and Toxins, helping to ensure safer use of our methods.
Ph. D.

Plant development is highly plastic, allowing plants to adapt to constant changes in environmental conditions. An excellent example of developmental plasticity is shoot branching. The final architecture of the shoot system is determined by the integration of environmental cues such as light and nutrients with endogenous cues. In this thesis the effect of Nitrogen (N) availability on Arabidopsis shoot branching was used as a model to investigate plant developmental plasticity. In particular, natural variation in shoot branching response to N supply was investigated using a set of multi parent advanced generation inter cross (MAGIC) lines (Kover et al., 2009). Correlations between traits in a selected group of MAGIC lines revealed several interesting correlations, characterising two strategies for N response. One strategy involved flowering early, maintaining branch numbers of low N, and minimal shift in resource allocation to roots. This was associated with good seed yield and yield retention on low N. An alternative strategy involves late flowering, high branching on high N but low branching on low N, (i.e. high branching plasticity), and a substantial increase in root fraction on Low N. This was associated with high seed yields on high N, but poor yield retention on low N. The molecular basis for these different strategies are currently unknown, but it seems likely that plant hormones are involved. Analysis of bud activation on isolated nodal stem segments provided strong evidence that the regulation of branching by N availability requires strigolactone (SL), and that strigolactone acts by increasing the competition between buds. There was some evidence of strigolatone resistance in a low plasticity MAGIC line. Shoot system architecture is a key factor underlying crop yield, and yield stability under low N input is an agricultural priority. Therefore, in parallel the branching responses of a set of Brassica rapa lines to N limitation were determined. Results highlight many conserved features between Arabidopsis and Brassica, as well as some differences. These comparisons should aid breeding for shoot system architectures that can deliver improved yield under low N.

Dystrophic epidermolysis bullosa results from mutations in COL7A1 that encodes collagen VII, the major component of anchoring fibrils. General paradigms have emerged attributing dominant DEB to heterozygous glycine substitutions and recessive DEB to nonsense, frameshift or splice site mutations on both COL7A1 alleles. Several aspects of the genotype-phenotype heterogeneity encountered in DEB remain unexplained, although genetic, epigenetic and environmental modulators have been implicated. In this thesis, various aspects of DEB were studied, in a bid to refine genotype-phenotype correlation. A detailed analysis of missense GS and non-GS mutations identified 57 novel mutations and was in-keeping with the general established paradigms. Unique clinical entities such as EB-pr and BDN were studied. The role of the matrix metalloproteinase-1 promoter polymorphism, -1607 1G/2G, on disease modification in EB-pr was explored, but was shown to be an unlikely modulator. A large study of BDN, highlighted that intracytoplasmic retention of collagen VII and stellate bodies were not exclusive to BDN and can be associated with various subtypes of DEB, non-EB cases and normal skin. The first case of revertant mosaicism in DEB was studied revealing intragenic cross-over as the underlying mechanism. Finally, intradermal injection of allogeneic fibroblasts was shown to result in increased and sustained expression of COL7A1 possibly through the upregulation of HB-EGF. Recognition of disease modifiers in DEB and refinement of genotype–phenotype correlation will not only further our understanding of DEB but will have implications on diagnosis, counselling and prognosis through patient specific and targeted therapy.

NeuroDevelopmental Disorders (NDDs) are a group of heterogeneous neuropsychiatric conditions, encompassing Developmental Delay (DD), Intellectual Disability (ID), Autism Spectrum Disorder (ASD) and Gilles de la Tourette Syndrome (GTS). NDDs often involve a life-long need of supportive services and represent a major economic and societal burden in Europe and the United States. Hitherto, no safe and effective treatment strategies are available, underpinning the urgency of deciphering their elusive aetiology. NDDs have a strong genetic component. Accordingly, the mechanistic understanding of disease involves (1) the description of mutational landscapes, (2) the molecular and cellular of characterisation of genetic variants and (3) their integration at circuit and system levels. In this thesis, we tackled these theoretical underpinnings to provide insights into the genetics of NDDs and the onset of associated clinical abnormalities. Firstly, aiming to shape the genetic architecture of GTS, a condition characterised by the presence of motor and vocal tics, we undertook a whole-genome CNV study of a cohort of Danish GTS cases and healthy controls. Using statistical and functional genomics approaches, we proposed novel potential candidate genes and implicated the disruption of early neurodevelopmental and late synaptic processes in the aetiology of GTS. Secondly, to elucidate the vast phenotypic heterogeneity of NDDs, we conducted a systematic investigation of genotype and phenotype relationships in DD, ID and ASD. Taking advantage of extensive phenotypic and genetic data available for DD/ID and ASD patients, we grouped individuals based on their functional rare CNV and gene disruptions but did not to identify distinguishing clinical archetypes. Instead, we showed converging molecular perturbations underlie the onset of globally more similar clinical presentations and investigated the role of common variants in modulating their expressivity. Lastly, we established the relevance of mouse models in the study of human disease. By applying comprehensive genomics approaches to over 1,000 mouse neuroanatomical knockouts, we implicated early neurodevelopmental and adult synaptic processes in the aetiology of ID and brain malformations. Furthermore, we showed that functionally converging genetic disturbances translate at the phenotypic level and proposed novel candidate ID genes.

Avec la révolution moléculaire en biologie, une compréhension des mécanismes de la relation génotype-phénotype est devenue possible. Récemment, les progrès réalisés dans la synthèse et le séquençage de l’ADN ont permis le développement d’expériences de deep-mutational scanning capable de quantifier divers phénotypes pour un ensemble de génotypes sur toute la longueur d’un gène. Ces ensembles de données sont non seulement intéressants en eux-mêmes, mais permettent également de tester de manière rigoureuse des modèles phénotypiques quantitatifs. Nous avons utilisé cette technologie pour caractériser les cartes séquence-fitness de 3 systèmes bactériens modèles: un régulateur global, la CRP, une enzyme de résistance aux antibiotiques, la β-lactamase, et une petite voie métabolique constituée des enzymes AraA et AraB. Ces systèmes ont été choisis pour éclairer les rôles de différentes caractéristiques dans la formation de la relation génotype-fitness (réseaux de régulations, stabilité des protéines et flux métabolique). Nous constatons que la tendance globale des effets sur le fitness semble prévaloir sur les tendances spécifiques. Ceci nous conduit à penser qu’une grande partie de la relation entre le génotype et le fitness pourrait être expliquée à partir de la forme des fonctions de phénotype-fitness. Par ailleurs, nous voyons que la caractérisation de la relation génotype-fitness dans différents systèmes peut être un moyen puissant d’obtenir des informations sur les phénotypes pertinents
With the molecular revolution in Biology, a mechanistic understanding of the genotype-phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep-mutational scanning experiments, capable of scoring comprehensive libraries of genotypes for a variety of phenotypes over the length of entire genes. Such datasets are not only interesting in themselves, but also allow rigorous testing of quantitative phenotypic models. We used this technology to characterise sequence-fitness maps for 3 model bacterial systems: a global regulator, CRP, an antibiotic-resistance enzyme, β-lactamase, and a small metabolic pathway, consisting of the enzymes AraA and AraB. These different systems were chosen to illuminate the roles of different mechanistic features in shaping the genotype-fitness relationship (regulatory wiring, protein stability and metabolic flux). We find that smooth patterns of fitness effects tend to prevail over idiosyncrasy, indicating that much of the genotype-fitness relationship could be understood from the global shape of smooth underlying phenotype-fitness functions. On the flip side, we see that characterising the genotype-fitness relationship in different systems can be a powerful way to glean phenotypic insights

In this thesis we develop a multi-scale model of the evolutionary dynamics of a population of cells, which accounts for the mapping between genotype and phenotype as determined by a model of the gene regulatory network. We study topological properties of genotype-phenotype networks obtained from the multi-scale model. Moreover, we study the problem of evolutionary escape and survival taking into account a genotype-phenotype map. An outstanding feature of populations with genotype-phenotype map is that selective pressures are determined by the phenotype, rather than genotypes. Our multi-scale model generates the evolution of a genotype-phenotype network represented by a pseudo-bipartite graph, that allows formulate a topological definition of the concepts of robustness and evolvability. We further study the problem of evolutionary escape for cell populations with genotype-phenotype map, based on a multi-type branching process. We present a comparative analysis between genotype-phenotype networks obtained from the multi-scale model and networks constructed assuming that the genotype space is a regular hypercube. We compare the effects on the probability of escape and the escape rate associated to the evolutionary dynamics between both classes of graphs. We further the study of evolutionary escape by analysing the long term survival conditioned to escape. Traditional approaches to the study of escape assume that the reproduction number of the escape genotype approaches infinity, and, therefore, survival is a surrogate of escape. Here, we analyse the process of survival upon escape by taking advantage of the fact that the natural setting of the escape problem endows the system with a separation of time scales: an initial, fast-decaying regime where escape actually occurs, is followed by a much slower dynamics within the (neutral network of) the escape phenotype. The probability of survival is analysed in terms of topological features of the neutral network of the escape phenotype.
En aquesta tesi es desenvolupa un model multi-escala de la dinàmica evolutiva d'una població de cèl·lules, tenint en compte la correspondència entre el genotip i el fenotip determinat per un model de la xarxa de regulació genètica. Estudiem les propietats topològiques de les xarxes genotip-fenotip obtingudes a partir del model multi-escala. D'altra banda, s'estudia el problema de la fugida evolutiva i la supervivència, tenint en compte una aplicació entre genotip i fenotip. Una característica destacable de les poblacions amb aplicació genotip-fenotip és que les pressions selectives actuen sobre els fenotips, en lloc dels genotips. El nostre model multi-escala genera l'evolució d'una xarxa genotip-fenotip representada per un graf pseudo-bipartit, el qual permet formular una definició topològica dels conceptes de robustesa y capacitat evolutiva. A més a més, estudiem el problema de fugida evolutiva de poblacions de cèl¿lules amb una aplicació genotip-fenotip, basat en en un procés de ramificació multi-tipus. Presentem un anàlisi comparatiu entre les xarxes de genotip-fenotip obtingudes a partir del model multi-escala i les xarxes construïdes assumint un espai de genotips de tipus hipercub regular. Comparem els efectes de la probabilitat de fugida i la freqüència d'escapament associades a la dinàmica evolutiva entre ambdues classes de grafs. Anem més enllà de l'estudi de fugida evolutiva mitjançant l'anàlisi de la supervivència a llarg plaç condicionat a fugir. Els enfocaments tradicionals per a l'estudi de la fugida o escapament suposen una taxa de reproducció en el genotip de fugida propera a infinit. Per tant, la supervivència és equivalent a la fugida. Aquí analitzem el procés de supervivència suposant fugida aprofitant el fet que l'entorn natural del problema de fugida dota al sistema amb una separació d'escales de temps: un règim inicial, de temps ràpid, on la fugida realment es produeix; seguit d'una dinàmica molt més lenta dins de la (xarxa neutra del) fenotip de fugida. La probabilitat de supervivència s'analitza en termes de les característiques topològiques de la xarxa neutra del fenotip de fugida

Hypertrophic cardiomyopathy (HCM) is an inherited disorder of cardiac muscle whose genetic basis has been investigated for over 25 years. However, considerable uncertainty remains about the genetic aetiology of HCM, including the validity of implicated genes, the effective analysis of variants detected in patients and the interpretation and follow-up of genetic testing results. Here, genetic data from large cardiomyopathy cohorts and 60,706 individuals of the Exome Aggregation Consortium (ExAC) was used to reassess the role of genes implicated in HCM and other cardiomyopathies. A significant excess of rare variation in cases over ExAC, along with supporting genetic evidence, was observed for only three non-sarcomeric genes, causative in < 2% of cases, with moderate evidence of association for five other non-sarcomeric genes. This data suggests HCM genetic testing should be limited to 16 valid genes, including the eight core sarcomeric genes. Variant analysis in sarcomeric genes has struggled to balance accuracy and sensitivity, with clinical genetics guidelines overly conservative in assigning pathogenicity. Here, by utilising stringent frequency thresholds and case-control analyses, classes of variants with high prior probabilities of pathogenicity (≥95%) were identified in five sarcomeric genes. By adapting current variant interpretation guidelines, the yield of pathogenic variants in HCM cases was increased by 14%, corresponding to 4% of all tested HCM patients. Building on this enhanced understanding of HCM genetics, genotype-phenotype analyses demonstrated that cases without causative variants follow a distinct clinical course, with later presentation, less pronounced fibrosis and markedly different hypertrophy patterns - lesser maximum wall thickness (19.85mm vs 18.51mm, p=0.006) but greater overall left ventricular mass (101.2g/m2 vs 88.6g/m2, p < 0.001). These results posit an informative interpretation of negative tests, indicating a benign prognosis and low likelihood of familial transmission. Taken together, these data redefine the genetic architecture of cardiomyopathy and significantly enhance the interpretability of HCM genetic testing.

Thesis (MScAgric) -- University of Stellenbosch, 2002.
ENGLISH ABSTRACT: Experiment 1: Two studies were conducted to research the effect of divergent selection for multiple rearing ability on carcass weight, mutton production, meat quality and carcass characteristics of similar-aged Merino sheep. Data of 114 19-month-old Merino sheep, 40 ewes and 74 rams were used in this study. The study was done in two parts over 2 years. Only rams (52) were slaughtered over a two-week period in study A. Twenty-two rams and 40 ewes were slaughtered over a three-week period in study B. The sheep were descended from two selection lines that have been divergently selected for maternal multiple rearing ability since 1986. In brief, ewe and ram progeny of ewes rearing more than one lamb per joining (i.e. that reared twins at least once) were preferred as replacements in the high (H) line. Descendants of ewes that reared fewer than one lamb per joining (i.e. that were barren or lost all lambs born at least once) were preferred as replacements in the low (L) line. In study A the mean (±SE) slaughter weight of H line rams . were 12% heavier (P0.05). The difference between the weight of the loin retail cut remained significant (P0.05). Hindquarter weight still remained significantly (PAFRIKAANSE OPSOMMING: Eksperiment 1: Twee studies is gedoen om te kyk na die invloed van seleksie vir meerling grootmaakvermoe by Merino's op karkas-, vleiseienskappe en vleiskwaliteit is. Data van 114 19 maand oue Merino skaap, 40 ooie en 74 ramme is in die studie gebruik. Die studie is gedoen in twee dele oar 'n tydperk van twee jaar. Slegs ramme (52) is geslag oor 'n tydperk van twee weke in studie A. Twee en twintig ramme en 40 ooie is in studie B geslag oor 'n pericde van drie weke. Merino-ooie en -ramme afkomstig van 'n hoe (Il-lyn) en lae (L-lyn) lyn geselekteer vir rneerling grootmaakverrnoe is gebruik in 'n studie wat oor twee jaar uitgevoer is. Die twee lyne is intensief geselekteer vir en teen meerling grootmaakverrnoe vanaf 1986. Ram- en ooi-nageslag wat afkomstig is van ooie wat een of meer keer tweelinge in haar lewe per lam kans groot gemaak het is gebruik vir die H-lyn, terwyl ram en ooi nageslag afkomstig van ooie wat een of minder as een lam per lamkans groot gemaak het is gebruik vir die L-Iyn. In studie A is 52 rarnme (42 H-Iyn en 10 Llyn) geslag en slag- en karkaseienskappe is bestudeer. In ondersoek B is 22 ramme (16 l-l-lyn en 6 L-lyn) en 40 coie (34 H-Iyn en 7 L-Iyn) gebruik. Slag-, karkas- en vleiseienskappe is bestudeer. In ondersoek A is gevind dat die slagmassa van die Il-Iyn ramme 12% hcer en die karkasmassa 13% hcer is as die van die L-lyn ramme. Na kovariansie ontleding van die swaarder slagmassa van die H-Iyn diere, was die pote (1.05±0.03 vs. 0.96±0.02 kg; P<0.05) en velie swazrder (3.93±0.15 vs. 3.34±0.07 kg; P