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Статті в журналах з теми "Multi-gene panel"

Автор: Grafiati

Опубліковано: 10 березня 2023

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1

Thakral, G., K. Vierkoetter, S. Namiki, S. Lawicki, X. Fernandez, K. Ige, W. Kawahara, and C. Lum. "AML multi-gene panel testing: A review and comparison of two gene panels." Pathology - Research and Practice 212, no. 5 (May 2016): 372–80. http://dx.doi.org/10.1016/j.prp.2016.02.004.

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2

de Biase, Dario, Giorgia Acquaviva, Michela Visani, Viviana Sanza, Chiara M. Argento, Antonio De Leo, Thais Maloberti, Annalisa Pession, and Giovanni Tallini. "Molecular Diagnostic of Solid Tumor Using a Next Generation Sequencing Custom-Designed Multi-Gene Panel." Diagnostics 10, no. 4 (April 23, 2020): 250. http://dx.doi.org/10.3390/diagnostics10040250.

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Next generation sequencing (NGS) allows parallel sequencing of multiple genes at a very high depth of coverage. The need to analyze a variety of targets for diagnostic/prognostic/predictive purposes requires multi-gene characterization. Multi-gene panels are becoming standard approaches for the molecular analysis of solid lesions. We report a custom-designed 128 multi-gene panel engineered to cover the relevant targets in 22 oncogene/oncosuppressor genes for the analysis of the solid tumors most frequently subjected to routine genotyping. A total of 1695 solid tumors were analyzed for panel validation. The analytical sensitivity is 5%. Analytical validation: (i) Accuracy: sequencing results obtained using the multi-gene panel are concordant using two different NGS platforms and single-gene approach sequencing (100% of 83 cases); (ii) Precision: consistent results are obtained in the samples analyzed twice with the same platform (100% of 20 cases). Clinical validation: the frequency of mutations identified in different tumor types is consistent with the published literature. This custom-designed multi-gene panel allows to analyze with high sensitivity and throughput 22 oncogenes/oncosuppressor genes involved in diagnostic/prognostic/predictive characterization of central nervous system tumors, non-small-cell lung carcinomas, colorectal carcinomas, thyroid nodules, pancreatic lesions, melanoma, oral squamous carcinomas and gastrointestinal stromal tumors.

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3

HAYASHI, SAORI, MAKOTO KUBO, SAWAKO MATSUZAKI, MASAYA KAI, TAKAFUMI MORISAKI, MAI YAMADA, KAZUHISA KANESHIRO, et al. "Significance of the Multi-gene Panel myRisk in Japan." Anticancer Research 42, no. 8 (July 26, 2022): 4097–102. http://dx.doi.org/10.21873/anticanres.15907.

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4

Hermel, David J., Wendy C. McKinnon, Marie E. Wood, and Marc S. Greenblatt. "Placing negative multi-gene panel results into clinical context." Familial Cancer 16, no. 4 (April 28, 2017): 595. http://dx.doi.org/10.1007/s10689-017-9974-0.

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5

Turriff, Amy E., Catherine A. Cukras, Brian P. Brooks, and Laryssa A. Huryn. "Considerations in multi-gene panel testing in pediatric ophthalmology." Journal of American Association for Pediatric Ophthalmology and Strabismus 23, no. 3 (June 2019): 163–65. http://dx.doi.org/10.1016/j.jaapos.2019.01.008.

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6

Khan, Arif O. "Considerations in multi-gene panel testing in pediatric ophthalmology." Journal of American Association for Pediatric Ophthalmology and Strabismus 24, no. 1 (February 2020): 57–58. http://dx.doi.org/10.1016/j.jaapos.2019.07.003.

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7

Christy, Joshua, Emad Kandah, Kavitha Kesari, and Trevor Singh. "Multi-gene mutation metastatic castrate-resistant prostate cancer." BMJ Case Reports 14, no. 7 (July 2021): e243124. http://dx.doi.org/10.1136/bcr-2021-243124.

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Gene panel sequencing of metastatic castrate-resistant prostate cancer (mCRPC) can assist in identifying appropriate targeted therapies. Although some studies have reported single DNA mutations, this is the first case of mCRPC with five different DNA mutations based on gene panel analysis. The patient, a 75-year-old man, initially presented with haematuria. Laboratory investigation revealed elevated prostate-specific antigen levels, and CT showed an enlarged prostate gland with metastatic lymph nodes. A 12-core biopsy revealed adenocarcinoma of the prostate. Gene panel sequencing demonstrated five different DNA mutations associated with sensitivities to olaparib and pembrolizumab. Treatment failure after hormonal therapy with leuprorelin and bicalutamide resulted in the initiation of chemotherapy with docetaxel. Over the past decade, development of genome sequencing analysis may guide us with more precise targeted therapy specific to mCRPC early on, especially with poly (ADP-ribose) polymerase inhibitors may show survival benefits.

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8

Senthilraja, Manickavasagam, Aaron Chapla, Felix K. Jebasingh, Dukhabhandhu Naik, Thomas V. Paul, and Nihal Thomas. "Parallel Multi-Gene Panel Testing for Diagnosis of Idiopathic Hypogonadotropic Hypogonadism/Kallmann Syndrome." Case Reports in Genetics 2019 (October 27, 2019): 1–3. http://dx.doi.org/10.1155/2019/4218514.

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Kallmann syndrome (KS)/Idiopathic hypogonadotropic hypogonadism (IHH) is characterized by hypogonadotropic hypogonadism and anosmia or hyposmia due to the abnormal migration of olfactory and gonadotropin releasing hormone producing neurons. Multiple genes have been implicated in KS/IHH. Sequential testing of these genes utilising Sanger sequencing is time consuming and not cost effective. The introduction of parallel multigene panel sequencing of small gene panels for the identification of causative gene variants has been shown to be a robust tool in the clinical setting. Utilizing multiplex PCR for the four gene KS/IHH panel followed by NGS, we describe herewith two cases of hypogonadotropic hypogonadism with a Prokineticin receptor 2 (PROKR2) gene and KAL1 gene mutation. The subject with a PROKR2 mutation had a normal perception of smell and normal olfactory bulbs on imaging. The subject with a KAL1 gene mutation had anosmia and a hypoplastic olfactory bulb.

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9

Schroeder, Christopher, Ulrike Faust, Marc Sturm, Karl Hackmann, Kathrin Grundmann, Florian Harmuth, Kristin Bosse, et al. "HBOC multi-gene panel testing: comparison of two sequencing centers." Breast Cancer Research and Treatment 152, no. 1 (May 29, 2015): 129–36. http://dx.doi.org/10.1007/s10549-015-3429-9.

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10

Ring, Kari Lassen, Amanda S. Bruegl, Brian Allen, Eric P. Elkin, Nanda Singh, Anne-Renee Hartman, and Russell Broaddus. "Multi-gene panel testing in an unselected endometrial cancer cohort." Journal of Clinical Oncology 33, no. 15_suppl (May 20, 2015): 1533. http://dx.doi.org/10.1200/jco.2015.33.15_suppl.1533.

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11

Kapoor, Nimmi S., Lisa D. Curcio, Carlee A. Blakemore, Amy K. Bremner, Rachel E. McFarland, John G. West, and Kimberly C. Banks. "Benefits and safety of multigene panel testing in patients at risk for hereditary breast cancer." Journal of Clinical Oncology 33, no. 28_suppl (October 1, 2015): 16. http://dx.doi.org/10.1200/jco.2015.33.28_suppl.16.

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16 Background: Recently introduced multi-gene panel testing including BRCA1 and BRCA2 genes (BRCA1/2) for hereditary cancer risk has raised concerns with the ability to detect all deleterious BRCA1/2 mutations compared to older methods of sequentially testing BRCA1/2 separately. The purpose of this study is to evaluate rates of pathogenic BRCA1/2mutations and variants of uncertain significance (VUS) between previous restricted algorithms of genetic testing and newer approaches of multi-gene testing. Methods: Data was collected retrospectively from 966 patients who underwent genetic testing at one of three sites from a single institution. Test results were compared between patients who underwent BRCA1/2testing only (limited group, n = 629) to those who underwent multi-gene testing with 5-43 cancer-related genes (panel group, n = 337). Results: Deleterious BRCA1/2 mutations were identified in 37 patients, with equivalent rates between limited and panel groups (4.0% vs 3.6%, respectively, p = 0.86). Thirty-nine patients had a BRCA1/2 VUS, with similar rates between limited and panel groups (4.5% vs 3.3%, respectively, p = 0.49). On multivariate analysis, there was no difference in detection of either BRCA1/2 mutations or VUS between both groups. Of patients undergoing panel testing, an additional 3.9% (n = 13) had non-BRCA pathogenic mutations and 13.4% (n = 45) had non-BRCA VUSs. Mutations in PALB2, CHEK2, and ATM were the most common non-BRCA mutations identified. Conclusions: Multi-gene panel testing detects pathogenic BRCA1/2 mutations at equivalent rates as limited testing and increases the diagnostic yield. Panel testing increases the VUS rate, mainly due to non-BRCA genes. Patients at risk for hereditary breast cancer can safely benefit from upfront, more efficient, multi-gene panel testing.

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12

Kapoor, Nimmi S., Jennifer Swisher, Rachel E. McFarland, Mychael Patrick, and Lisa D. Curcio. "Impact of hereditary multigene panel testing for cancer survivors." Journal of Clinical Oncology 34, no. 3_suppl (January 20, 2016): 261. http://dx.doi.org/10.1200/jco.2016.34.3_suppl.261.

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261 Background: Recently, genetic testing for hereditary cancer syndromes has seen numerous advances in testing spectrum, capability, and efficiency. This may have important implications for cancer survivors and their families. The purpose of this study is to evaluate the impact of reflex genetic testing with newer multi-gene panels on patients with prior negative BRCA1/2 tests. Methods: Data was collected retrospectively from patients who underwent multi-gene panel testing at one of three sites from a single institution between 8/2013-6/2015. Those with a personal history of breast or ovarian cancer and a prior negative BRCA1/2 test were included. Results: Of 914 patients who underwent multi-gene panel tests, 187 met study inclusion criteria. Ten patients (5.3%) were found to carry 11 pathogenic mutations, including 6 patients with mutations in CHEK2, 2 patients with mutations in PTEN, and 1 patient each with mutations in the following genes: BARD1, NF1, and RAD51C. One patient had two pathogenic mutations identified—CHEK2 and BARD1. Of 10 patients with mutations, 9 had a personal history of breast cancer diagnosed at a median age of 43 (range 35-52) and 1 had ovarian cancer diagnosed at age 65. A majority of mutation carriers underwent panel testing years after their cancer diagnosis (median 6 years, range 0.5-32 years) and none with delayed testing had undergone prophylactic contralateral mastectomy prior to the discovery of their gene mutation. All patients with mutations had a family history of at least one cancer, with most having a variety of cancer diagnoses in multiple relatives. Positive panel testing results altered clinical management in most patients, including addition of breast MRI, colonoscopy, or thyroid ultrasound depending on the gene mutation. After discovery of a PTEN mutation 19 years after her initial cancer treatment, one woman underwent bilateral prophylactic mastectomy and was found to have occult ductal carcinoma in situ. Conclusions: Cancer survivorship must incorporate advances in technology that may be beneficial even years after treatment has ended. Multi-gene panel testing can be applied in survivorship settings as a useful tool to guide screening recommendations.

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13

Fanale, Daniele, Lorena Incorvaia, Clarissa Filorizzo, Marco Bono, Alessia Fiorino, Valentina Calò, Chiara Brando, et al. "Detection of Germline Mutations in a Cohort of 139 Patients with Bilateral Breast Cancer by Multi-Gene Panel Testing: Impact of Pathogenic Variants in Other Genes beyond BRCA1/2." Cancers 12, no. 9 (August 25, 2020): 2415. http://dx.doi.org/10.3390/cancers12092415.

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Patients with unilateral breast cancer (UBC) have an increased risk of developing bilateral breast cancer (BBC). The annual risk of contralateral BC is about 0.5%, but increases by up to 3% in BRCA1 or BRCA2 pathogenic variant (PV) carriers. Our study was aimed to evaluate whether all BBC patients should be offered multi-gene panel testing, regardless their cancer family history and age at diagnosis. We retrospectively collected all clinical information of 139 BBC patients genetically tested for germline PVs in different cancer susceptibility genes by NGS-based multi-gene panel testing. Our investigation revealed that 52 (37.4%) out of 139 BBC patients harbored germline PVs in high- and intermediate-penetrance breast cancer (BC) susceptibility genes including BRCA1, BRCA2, PTEN, PALB2, CHEK2, ATM, RAD51C. Nineteen out of 53 positively tested patients harbored a PV in a known BC susceptibility gene (no-BRCA). Interestingly, in the absence of an analysis performed via multi-gene panel, a significant proportion (14.4%) of PVs would have been lost. Therefore, offering a NGS-based multi-gene panel testing to all BBC patients may significantly increase the detection rates of germline PVs in other cancer susceptibility genes beyond BRCA1/2, avoiding underestimation of the number of individuals affected by a hereditary tumor syndrome.

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14

Wang, Qiang, Ning Zhao, and Jun Zhang. "Gene Mutation Analysis in Papillary Thyroid Carcinoma Using a Multi-Gene Panel in China." International Journal of General Medicine Volume 14 (September 2021): 5139–48. http://dx.doi.org/10.2147/ijgm.s327409.

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15

Horton, Carolyn, Marcy Richardson, Kate Durda, Amal Yussuf, Michelle Jackson, Kory Jasperson, Yuan Tian, Holly LaDuca, and Tobias Else. "Universal Multi Gene Panel Testing For Individuals With Pheochromocytomas And Paragangliomas." Journal of the Endocrine Society 5, Supplement_1 (May 1, 2021): A512—A513. http://dx.doi.org/10.1210/jendso/bvab048.1048.

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Abstract Background: Pheochromocytomas (PCCs) and paragangliomas (PGLs) (PPGLs) are a genetically heterogeneous entity, with roughly 25-40% of cases found to harbor a pathogenic or likely pathogenic germline alteration. Existing practice guidelines advocating for the use of a sequential gene testing strategy to identify individuals with hereditary PPGL are driven by the presence of specific clinical features and predate the routine use of multigene panel testing (MGPT). Here we describe results of MGPT for hereditary PPGL in a clinically and ancestrally diverse cohort from a diagnostic laboratory. Methods: Demographic and clinical information of individuals undergoing targeted MGPT for hereditary PPGL were collected from test requisition forms and supporting clinical documents provided by the ordering clinician and retrospectively reviewed. Individuals underwent MGPT of 10-12 genes depending on test order date. From August 2013 through May 2015, 560 individuals had targeted MGPT that included 10 genes (NF1, MAX, SDHA/B/C/D/AF2, RET, TMEM127, and VHL), and from May 2015 through December 2019, 1167 individuals had panel testing of 12 genes due to the addition of MEN1 and FH. Results: Overall, 27.5% of individuals had a pathogenic or likely pathogenic variant (PV), 9.0% had a variant of uncertain significance, and 63.1% had a negative result. Out of all PVs, most were identified in SDHB (40.4%), followed by SDHD (21.1%), SDHA (10.1%), VHL (7.8%), SDHC (6.7%), RET (3.8%), and MAX (3.6%). PVs in FH, MEN1, NF1, SDHAF2, and TMEM127 collectively accounted for 6.5% of PVs. Clinical predictors of a PV included extra-adrenal location, diagnosis before the age of 45 years, multiple tumors, and positive family history (fhx) of PPGL. Affected individuals with a fhx of PPGL were the most likely to have a PV (70.6% of individuals with PCC + fhx; 85.9% of individuals with PGL + fhx). The positive rate in nearly all clinical subgroups even without predictors of a PV remained over 10%, including individuals with a single tumor (PCC = 16.7%; PGL = 46.7%) and those without a fhx (PCC and negative fhx = 15.8%; PGL and negative fhx = 43.7%). Restricting genetic testing of hereditary PPGL to only SDHB/C/D genes misses a third (31.8%) of individuals with PVs. Among individuals with PVs in syndromic genes, over half (41.5%) did not have any additional syndromic features beyond PPGL reported by the ordering clinician. Conclusion: Our data demonstrate a high diagnostic yield in individuals with and without established risk factors, a low inconclusive result rate, numerous individuals with syndromic PVs presenting with isolated PPGL, and a substantial contribution to diagnostic yield from rare genes when included in testing. These findings support updating practice guidelines to incorporate universal testing of all individuals with PPGL and the use of concurrent MGPT as the ideal platform.

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16

Horton, Carolyn, Kate Durda, Michelle Jackson, Marcy Richardson, Yuan Tian, Holly LaDuca, Kory Jasperson, and Tobias Else. "Universal multi-gene panel testing for individuals with pheochromocytomas and paragangliomas." Molecular Genetics and Metabolism 132 (April 2021): S54—S55. http://dx.doi.org/10.1016/s1096-7192(21)00165-7.

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17

Sutcliffe, Erin G., Amanda Bartenbaker Thompson, Amy R. Stettner, Megan L. Marshall, Maegan E. Roberts, Lisa R. Susswein, Ying Wang, Rachel T. Klein, Kathleen S. Hruska, and Benjamin D. Solomon. "Multi-gene panel testing confirms phenotypic variability in MUTYH-Associated Polyposis." Familial Cancer 18, no. 2 (January 2, 2019): 203–9. http://dx.doi.org/10.1007/s10689-018-00116-2.

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18

Cutting, Elizabeth, Meghan Banchero, Amber L. Beitelshees, James J. Cimino, Guilherme Del Fiol, Ayse P. Gurses, Mark A. Hoffman, et al. "User-centered design of multi-gene sequencing panel reports for clinicians." Journal of Biomedical Informatics 63 (October 2016): 1–10. http://dx.doi.org/10.1016/j.jbi.2016.07.014.

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19

Wang, Louise, John T. Nathanson, Jessica Long, Jessica Ebrahimzadeh, Shria Kumar, Kirk J. Wangensteen, Bryson W. Katona, and Anil K. Rustgi. "Tu1673 – Single-Gene Vs. Multi-Gene Panel Testing in Management of Hereditary Gastrointestinal Cancer Syndromes." Gastroenterology 156, no. 6 (May 2019): S—1086. http://dx.doi.org/10.1016/s0016-5085(19)39677-5.

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20

Olopade, Olufunmilayo I., Sarah Nielsen, Shengfeng Wang, Ryan Bernhisel, Krystal Brown, Hannah C. Cox, Shelly Cummings, et al. "Ancestry-based differences in hereditary cancer genetic testing." Journal of Clinical Oncology 35, no. 15_suppl (May 20, 2017): e13107-e13107. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.e13107.

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e13107 Background: Ancestry-based disparities in genetic testing for the hereditary breast and ovarian cancer (HBOC) genes BRCA1/2 have been well documented, but it is unclear whether this extends to other cancer-risk genes. Given reduced costs and broader access to multi-gene panels, we evaluated ancestry-based differences in the utilization and outcomes of HBOC and pan-cancer panel testing. Methods: Individuals who had genetic testing for BRCA1/2only (2006-2016) or with a multi-gene pan-cancer panel (2013-2016) were assessed. Clinical information was obtained from provider-completed test request forms. The most commonly reported ancestries [European (EU), Latin American/Caribbean (LA/C), African (AF), Asian (AS)] were evaluated. Individuals of Ashkenazi Jewish ancestry were not included in the EU group. Results: The relative utilization of HBOC testing in 2013-2016 increased in AF and LA/C individuals (vs 2006-2013) and was similar to panel testing in all ancestries (Table). The positive mutation rate for panel testing was 6.7%; AF (6.4%), LA/C (6.6%), AS (7.1%), EU (7.1%). The positive rate for HBOC testing from 2006-2013 was 5.7%. Of significance, the HBOC positive rate from 2013-2016 dropped to 4.1% and ancestry-specific positive rates were much lower relative to panel testing (Table). Gene-specific mutation prevalence differed by ancestry, but mutations were identified in a wide range of genes for all ancestries. Possible founder mutations were identified in BRCA1/2 and other genes. Conclusions: In this cohort, broader access to genetic testing has reduced disparities in recent years and panel testing shows improved clinical utility relative to HBOC testing in all ancestries. [Table: see text]

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21

Reid, Sonya, and Tuya Pal. "Update on multi‐gene panel testing and communication of genetic test results." Breast Journal 26, no. 8 (July 8, 2020): 1513–19. http://dx.doi.org/10.1111/tbj.13971.

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22

Sbardella, Emilia, Treena Cranston, Andrea M. Isidori, Brian Shine, Aparna Pal, Bahram Jafar-Mohammadi, Greg Sadler, Radu Mihai, and Ashley B. Grossman. "Routine genetic screening with a multi-gene panel in patients with pheochromocytomas." Endocrine 59, no. 1 (May 5, 2017): 175–82. http://dx.doi.org/10.1007/s12020-017-1310-9.

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23

Zhunussova, G., G. Afonin, S. Abdikerim, A. Jumanov, A. Perfilyeva, D. Kaidarova, and L. Djansugurova. "NGS-based multi-gene panel analysis in early-onset colorectal cancer patients." Annals of Oncology 30 (November 2019): vii16—vii17. http://dx.doi.org/10.1093/annonc/mdz413.059.

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24

Cadoo, Karen Anne, Deborah DeLair, Diana Mandelker, Richard R. Barakat, Carol L. Brown, Dennis Chi, Ginger J. Gardner, et al. "Multi gene panel testing in unselected patients (pts) with endometrial cancer (EC)." Journal of Clinical Oncology 35, no. 15_suppl (May 20, 2017): e17119-e17119. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.e17119.

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e17119 Background: Inherited mutations (muts) in Lynch Syndrome genes (LS) & PTEN are associated with EC. The prevalence of other cancer predisposition genes is unclear. The majority of studies have selected pts by age, family history or specific tumor features. We sought the prevalence of cancer predisposition genes in unselected pts attending for surgical consultation. Methods: 03/2016-10/2016, pts with new EC diagnosis were offered to consent to an IRB approved protocol. Tumor-normal sequencing, was performed via a custom next-generation sequencing panel (MSK-IMPACT) with return of results for 76 cancer predisposition genes. Per institutional standard, all ECs undergo reflex screening for LS with IHC for mismatch repair proteins (MMR P). Results:77 pts consented, median age 60 (27-84), median BMI 27 (16-66), 27% Ashkenazi Jewish (AJ) descent. Tumors: 56 (73%) stage 1, remainder stage 3 or 4, majority (52, 68%) endometrioid histology, of which 31 (60%) grade 1. 15 pathogenic germline variants were identified in 14 pts (18%) including 3 (4%) in LS genes (2 MSH6, 1 MLH1) with corresponding abnormal MMR P. One pt with a known BRCA1 mutation, without prior cancer, with prior risk reducing salpingo-oophorectomy had stage III grade 3 endometrioid EC at 47 yo, tumor LOH at BRCA1 was identified. Of the 4 pts with high-penetrance muts, 3 met criteria for genetic testing for the implicated gene due to personal/family cancer history, 1 pt with MSH6 mutation was identified via absent MMR P only. The remaining 11 pathogenic variants were incremental findings in moderate penetrance ( CHEK2 I157T, MRE11, ATM, APC I1307K, MUTYH) or autosomal recessive genes ( MUTYH, RECQL4, ATM). 5 pt had moderate penetrance variants in known AJ founder muts. Conclusions: In this cohort of unselected EC pts the prevalence of LS was as expected & reflex IHC screening captured all pts appropriately. While all high-penetrance muts were captured by clinical criteria, the incremental identification of moderate penetrance muts in these largely early stage/ low risk EC pts may alter personal & at-risk family member breast & colon cancer screening recommendations. Continuing accrual will reveal the extent to which additional high penetrance genes are seen in unselected EC pts.

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Brown, Krystal, Gregory Sampang Calip, Ryan Bernhisel, Brent Evans, Eric Thomas Rosenthal, Jennifer Saam, Johnathan Lancaster, and Kent Hoskins. "Multi-gene hereditary cancer testing among men with breast cancer." Journal of Clinical Oncology 35, no. 15_suppl (May 20, 2017): 1532. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.1532.

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1532 Background: All men with a personal diagnosis of breast cancer (BC) are candidates for BRCA1/2 genetic testing, as pathogenic variants (PVs) in these genes have a known association with BC risk in both men and women. As additional genes with known BC risk in women are now routinely included in multi-gene panel testing, we evaluated the outcomes of multi-gene panel testing in a large cohort of men with BC. Methods: This analysis includes the results of commercial genetic testing for 1,358 men with BC usinga multi-gene pan-cancer panel between September 2013 and January 2017. Clinical information was obtained from provider-completed test request forms. Age at diagnosis, personal, and family history were compared for men with PVs in BRCA1/2 versus non- BRCA1/2 genes. Results: Overall, 207 (15.2%) men with BC were found to carry a PV, where 147 (10.8%) men had a PV in BRCA1/2 ( BRCA1, 0.7%; BRCA2, 10.2%) and 60 (4.4%) men had a PV in a non- BRCA1/2 gene ( CHEK2, 2.0%; ATM, 1.0%; PALB2, 1.0%; BARD1, 0.2%; NBN, 0.2%; MSH6, 0.1%; BRIP1, 0.1%; CDH1, 0.1%; CDKN2A, 0.1%; MLH1, 0.1%, TP53, 0.1%). There were no substantial differences in the median age-at-diagnosis for men without a PV (65) compared to those with a BRCA1/2 PV (66) or a non- BRCA1/2 PV (63). Prostate cancer was the most common additional malignancy among all men with BC (9.0%), with a similar incidence among men with a BRCA1/2 PV (9.2%) and a non- BRCA1/2 PV (8.3%). In addition, 1.4% of men with a BRCA1/2 PV and 3.3% of men with a non- BRCA1/2 PV had a second BC. A family history of breast and/or ovarian cancer was present in 44.4% of the testing cohort, 66.7% of men with a BRCA1/2 PV, and 48.3% of men with a non- BRCA1/2 PV. This is consistent with the relative penetrance of BRCA1/2 and other genes included here. There were no other substantial differences in family history among BRCA1/2 PV carriers versus non- BRCA1/2 PV carriers. Conclusions: Close to a third of all PVs identified here in men with BC were in a gene other than BRCA1/2. There were no obvious differences in the clinical presentation of men with a BRCA1/2 PV compared to men with a PV in another gene or no PV at all. Collectively, this suggests that multi-gene panel testing is appropriate for all men with BC, regardless of other personal or family history.

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Gieldon, Laura, Jimmy Rusdian Masjkur, Susan Richter, Roland Därr, Marcos Lahera, Daniela Aust, Silke Zeugner, et al. "Next-generation panel sequencing identifies NF1 germline mutations in three patients with pheochromocytoma but no clinical diagnosis of neurofibromatosis type 1." European Journal of Endocrinology 178, no. 2 (February 2018): K1—K9. http://dx.doi.org/10.1530/eje-17-0714.

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Objective Our objective was to improve molecular diagnostics in patients with hereditary pheochromocytoma and paraganglioma (PPGL) by using next-generation sequencing (NGS) multi-gene panel analysis. Derived from this study, we here present three cases that were diagnosed with NF1 germline mutations but did not have a prior clinical diagnosis of neurofibromatosis type 1 (NF1). Design We performed genetic analysis of known tumor predisposition genes, including NF1, using a multi-gene NGS enrichment-based panel applied to a total of 1029 PPGL patients. We did not exclude genes known to cause clinically defined syndromes such as NF1 based on missing phenotypic expression as is commonly practiced. Methods Genetic analysis was performed using NGS (TruSight Cancer Panel/customized panel by Illumina) for analyzing patients’ blood and tumor samples. Validation was carried out by Sanger sequencing. Results Within our cohort, three patients, who were identified to carry pathogenic NF1 germline mutations, attracted attention, since none of the patients had a clinical suspicion of NF1 and one of them was initially suspected to have MEN2A syndrome due to co-occurrence of a medullary thyroid carcinoma. In these cases, one splice site, one stop and one frameshift mutation in NF1 were identified. Conclusions Since phenotypical presentation of NF1 is highly variable, we suggest analysis of the NF1 gene also in PPGL patients who do not meet diagnostic NF1 criteria. Co-occurrence of medullary thyroid carcinoma and PPGL was found to be a clinical decoy in NF1 diagnostics. These observations underline the value of multi-gene panel NGS for PPGL patients.

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Sorscher, Steven M. "Estimating risk using multi-gene panel testing; do negative results change the risk?" Journal of Human Genetics 62, no. 2 (October 13, 2016): 339. http://dx.doi.org/10.1038/jhg.2016.125.

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Lee, Cha Gon, Jeehun Lee, and Munhyang Lee. "Multi-gene panel testing in Korean patients with common genetic generalized epilepsy syndromes." PLOS ONE 13, no. 6 (June 20, 2018): e0199321. http://dx.doi.org/10.1371/journal.pone.0199321.

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Steuten, L., B. Goulart, N. Meropol, D. Pritchard, and S. D. Ramsey. "PCN93 COST-EFFECTIVENESS OF MULTI-GENE PANEL SEQUENCING FOR PATIENTS WITH ADVANCED MELANOMA." Value in Health 22 (May 2019): S73. http://dx.doi.org/10.1016/j.jval.2019.04.217.

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Kelly, Patricia A. "Next Generation Sequencing and Multi-Gene Panel Testing: Implications for the Oncology Nurse." Seminars in Oncology Nursing 33, no. 2 (May 2017): 208–18. http://dx.doi.org/10.1016/j.soncn.2017.02.007.

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Ring, Kari L., Amanda S. Bruegl, Brian A. Allen, Eric P. Elkin, Nanda Singh, Anne-Renee Hartman, Molly S. Daniels, and Russell R. Broaddus. "Germline multi-gene hereditary cancer panel testing in an unselected endometrial cancer cohort." Modern Pathology 29, no. 11 (July 22, 2016): 1381–89. http://dx.doi.org/10.1038/modpathol.2016.135.

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Shah, Kanisha, Shanaya Patel, Sheefa Mirza, and Rakesh M. Rawal. "A multi-gene expression profile panel for predicting liver metastasis: An algorithmic approach." PLOS ONE 13, no. 11 (November 1, 2018): e0206400. http://dx.doi.org/10.1371/journal.pone.0206400.

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Sutcliffe, Erin G., Amy R. Stettner, Stacey A. Miller, Sheila R. Solomon, Megan L. Marshall, Maegan E. Roberts, Lisa R. Susswein, et al. "Differences in cancer prevalence among CHEK2 carriers identified via multi-gene panel testing." Cancer Genetics 246-247 (August 2020): 12–17. http://dx.doi.org/10.1016/j.cancergen.2020.07.001.

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Russo, Roberta, Immacolata Andolfo, Francesco Manna, Antonella Gambale, Roberta Marra, Barbara Eleni Rosato, Paola Caforio, et al. "Multi-gene panel testing improves diagnosis and management of patients with hereditary anemias." American Journal of Hematology 93, no. 5 (February 24, 2018): 672–82. http://dx.doi.org/10.1002/ajh.25058.

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Cock-Rada, A. M., C. A. Ossa, H. I. Garcia, and L. R. Gomez. "A multi-gene panel study in hereditary breast and ovarian cancer in Colombia." Familial Cancer 17, no. 1 (May 20, 2017): 23–30. http://dx.doi.org/10.1007/s10689-017-0004-z.

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Sorscher, Steven M. "Patients with negative multi-gene panel testing: a back to the future paradox?" Familial Cancer 16, no. 3 (March 3, 2017): 459. http://dx.doi.org/10.1007/s10689-017-9967-z.

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Azam, Sarah, Krista Qualmann, Syed Hashmi, Aarti Ramdaney, David Rodriguez-Buritica, Leslie Dunnington, and Michelle Jackson. "GENE-04. CHARACTERISTICS OF PATIENTS WITH A PRIMARY BRAIN TUMOR UNDERGOING HEREDITARY CANCER MULTI-GENE PANEL TESTING." Neuro-Oncology 20, suppl_6 (November 2018): vi103. http://dx.doi.org/10.1093/neuonc/noy148.431.

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Blazer, Kathleen R., Carin Espenschied, Benjamin Weissman, Sharon Sand, and Jeffrey N. Weitzel. "Next-generation sequencing for genetic cancer risk assessment: Critical needs and perceptions of community clinicians." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): 1536. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.1536.

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1536 Background: Current standard-of-care practice for genetic cancer risk assessment (GCRA) focuses on single-gene testing for specific hereditary cancer syndromes. Next-generation sequencing (NGS) technologies recently became available for clinical applications. This study explored the perspectives and experiences of community-based clinicians regarding NGS testing for personalized GCRA. Methods: A 27-item survey was developed and administered online to 325 members of an interdisciplinary nationwide clinical cancer genetics community of practice. Results: Of 94 (29%) respondents, 25 (27%) have ordered at least one multi-gene panel and only 2 (2.1%) have ordered a whole exome or genome test from a commercial vendor for GCRA. Concerns about clinical utility, the challenge of interpreting and communicating results, lack of knowledge about and potential costs were most often cited as reasons for not pursuing NGS testing. Respondents were significantly more confident about their ability to interpret and counsel about single gene test results compared with multi-gene panels or whole exome/genome sequencing; and about multi-gene panels over whole exome/genome sequencing (p<.0001 for all comparisons). Conclusions: Findings suggest that while NGS tests are entering the realm of GCRA, multidisciplinary genomics education and clinical support resources are needed to address barriers to utilization and promote successful integration of NGS testing into community-based GCRA practice settings.

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Song, Yuntao, Bin Zhang, and Tonghui Ma. "Highly accurate NGS-based multi-gene testing in the diagnosis of thyroid nodules with indeterminate cytology." Journal of Clinical Oncology 38, no. 15_suppl (May 20, 2020): e13579-e13579. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e13579.

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e13579 Background: Thyroid nodules are highly prevalent, Fine-needle aspiration (FNA) is the standard pre-operative tool for diagnosis. However, some of the samples are classified as indeterminate, which leads to unnecessary surgery. BRAF V600E mutation is often used as a diagnostic marker for thyroid cancer, and it is highly specific for papillary thyroid carcinoma (PTC). But BRAF mutation is rarely occurred in thyroid nodules with indeterminate cytology. To diagnose the indeterminate thyroid nodules precisely, some NGS-based multi-gene testing panel has been developed and clinically used in America and Europe, but rare research was reported in China. In this study, we evaluated the value of a next-generation sequencing (NGS) panel to cancer diagnosis in indeterminate thyroid nodules. Methods: From February 2018 to September 2018, 360 patients with thyroid nodules who underwent FNA at Peking University Cancer Hospital were enrolled. And the FNA samples with indeterminate cytology were evaluated using a next-generation sequencing (NGS) assay, including 16 genes analyzed for point mutations and 26 types of gene fusions. Diagnostic performance of this multi-gene testing panel was compared with BRAF V600E single gene mutation analysis. Results: 141 nodules were cytologically indeterminate among 360 patients on FNA biopsy, 72 of which were resected and analyzed by NGS successfully. Histologic analysis after surgery revealed 41 (56.9%) cancers in these 72 patients. The multi-gene testing assay could classify 30/41 cancers correctly, showing a sensitivity of 73.2%, specificity of 96.8%, positive predictive value of 96.8%, and negative predictive value of 73.2%. The diagnostic accuracy of the multi-gene testing was significantly higher than the BRAF V600E mutation analysis (83.3% vs 73.6%, x2= 31.588, p < 0.01). Conclusions: Our study demonstrated that the multi-gene testing provided both high sensitivity and high specificity for cancer detection in thyroid nodules with indeterminate cytology, and its accuracy was much higher than BRAF V600E mutation test.

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Lee, Byung-In, Kahuku Oades, Lien Vo, Jerry Lee, Mark Landers, Yipeng Wang, and Joseph Monforte. "NGS-based targeted RNA sequencing for expression analysis of patients with triple-negative breast cancer using a modulized, 96-gene biomarker panel." Journal of Clinical Oncology 30, no. 30_suppl (October 20, 2012): 56. http://dx.doi.org/10.1200/jco.2012.30.30_suppl.56.

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56 Background: Gene expression profiling has been shown to be effective in analyzing postoperative tumor samples in various cancers. However, in analyzing small specimens such as core biopsies, the limited amount of available material makes multi-gene analyses difficult or impossible. Microarray-based analyses also provide limited dynamic range. We describe the development of targeted RNA-sequencing methodology which combines the power of a universal RNA amplification with NGS for an ultra-deep expression analysis of multiple target genes, enabling <100 ng of sample input for multi-gene analysis in a single tube format. Methods: The gene expression patterns of triple-negative breast cancer FFPE samples were analyzed using a 96-gene breast cancer biomarker panel across three different platforms: Affymetrix Human Gene ST 1.0 microarrays, a pre-developed OncoScore qRT-PCR panel, and targeted RNA-seq. For targeted RNA-seq analysis, the 96-gene panel was amplified using a universal, single-tube “XP-PCR” amplification strategy followed by sequence analysis using the Ion-Torrent Personal Genome Machine. Results: Targeted RNA-seq provided the most sensitivity in terms of detection rates with <100 ng FFPE RNA input and provides unlimited dynamic range with increased sequencing depth. Expression ratio compression issues typically associated with a high number of pre-amplification cycles in standard multiplex-primed methods were not observed here. Low expressing genes, undetectable by qRT-PCR analysis from 1,000 ng input FFPE RNA, were detected and eligible for expression analysis with a significant number of sequencing reads. Alternative transcription/splicing analysis is also possible from sequence analysis of the target transcripts using targeted RNA-seq. Conclusions: By combining universally primed pre-amplification and NGS in multi-gene expression analysis, targeted RNA-seq provides the most sensitive gene expression analysis methodology.

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Mizoguchi, Masahiro, Nobuhiro Hata, Daisuke Kuga, Ryusuke Hatae, Yuhei Sangatsuda, Yutaka Fujioka, Kosuke Takigawa, Yusuke Funakoshi, and Yuhki Koga. "MPC-06 Cutting-edge of Cancer Genomic Medicine for brain tumors." Neuro-Oncology Advances 2, Supplement_3 (November 1, 2020): ii12. http://dx.doi.org/10.1093/noajnl/vdaa143.051.

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Abstract Kyushu University Hospital was designated a Cancer Genome Core Hospital in April 2018, and the multi-gene panel test has been introduced since August 2019. The expert panel has been held for 21 cases of the central nervous system (11 adult glioma, 5 pediatric brain tumors, 5 extramedullary tumors). Actionable gene abnormalities were newly detected in two cases. First case is epithelioid glioblastoma with BRAF V600E mutation, and second is embryonal tumor with VCL-ALK fusion. For the first case, BRAF/MEK inhibitor can be used by the prospective trial of patient-proposed healthcare services with multiple targeted agent based on the result of gene profiling by multigene panel test (NCCH1901). For the second case, we are planning to introduce ALK inhibitor by indicator-initiated clinical trial while continuing ICE therapy. The current approved agents for tumor-agnostic treatment are immune checkpoint inhibitors for mismatch repair deficient (dMMR) cases and TRK inhibitors for NTRK fusion gene-positive cases. We selected microsatellite instability (MSI) test and immunostaining of MMR gene for the indication of immune checkpoint inhibitor for recurrent glioma and Lynch syndrome that require dMMR evaluation, but FoundationOne CDx (F1CDx) allows simultaneous evaluation of MSI and MMR gene abnormalities. Regarding the indication of TRK inhibitors, F1CDx assay is selected as a companion diagnosis for ALK, NTRK1/2/3 fusion gene analysis for pediatric cases. At present, the actionable gene abnormalities are detected by multi-gene panel tests in about 10% of brain tumors. Development of tumor-agnostic treatment will expand the molecular target therapy for brain tumor in the future. Based on the experience of different schemes for molecular targeted therapy, it became clear that it is necessary to establish a cancer genome medical system for prompt introduction of precision medicine for highly malignant brain tumors.

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Fehm, Tanja N., Christina Blassl, Jan Dominik Kuhlmann, Alessandra Webers, Pauline Wimberger, and Hans Neubauer. "Gene expression profiling of single circulating tumor cells in ovarian cancer: Establishment of a multi-marker gene panel." Journal of Clinical Oncology 34, no. 15_suppl (May 20, 2016): e17085-e17085. http://dx.doi.org/10.1200/jco.2016.34.15_suppl.e17085.

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Blassl, Christina, Jan Dominik Kuhlmann, Alessandra Webers, Pauline Wimberger, Tanja Fehm, and Hans Neubauer. "Gene expression profiling of single circulating tumor cells in ovarian cancer - Establishment of a multi-marker gene panel." Molecular Oncology 10, no. 7 (April 20, 2016): 1030–42. http://dx.doi.org/10.1016/j.molonc.2016.04.002.

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Welinsky, Sara, Emily Soper, George Diaz, and Aimee L. Lucas. "Prevalence of Gene Mutations in Patients at Increased Risk of Pancreatic Cancer: Impact of Multi-Gene Panel Testing." Gastroenterology 152, no. 5 (April 2017): S556. http://dx.doi.org/10.1016/s0016-5085(17)32016-4.

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45

Hall, Michael J., Michelle J. McSweeny, Kim Rainey, Hannah Campbell, Chau Nguyen, and Catherine Neumann. "Risks and implications of multiple actionable pathogenic germline variants discovered by panel-based cancer predisposition testing." Journal of Clinical Oncology 41, no. 4_suppl (February 1, 2023): 792. http://dx.doi.org/10.1200/jco.2023.41.4_suppl.792.

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792 Background: Multi-gene hereditary cancer panels have revolutionized how patients with germline mutations are identified by testing multiple genes at the same time. Despite the availability of panel testing, many patients with a known familial mutation will only undergo single site genetic testing due to limitations in guideline recommendations and insurance coverage. This approach risks a failure to detect additional pathogenic variants and an inappropriate management of cancer risk. In our clinical experience, a subset of patients pursue multigene testing despite a known familial mutation. Our group has identified patients who carry more than one mutation and mutations that would have been missed if the patients had only undergone single site testing. We investigated the patients and families from our risk assessment clinic with multiple familial mutations and determined how medical management may have been changed due to the presence of multiple mutations in family. Methods: The Fox Chase Cancer Center Risk Assessment Program (RAP) Registry was queried to identify patients who carry more than one mutation. Pedigrees of patients and families identified with multiple germline mutations were reviewed. Screening management guidelines were determined from the most recent NCCN guidelines published at the time the patient tested (Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic and Genetic/Familial High-Risk Assessment: Colorectal). The RAP Registry is an IRB approved protocol (IRB 09-831). Results: 70 patients were found to carry at least 2 mutations (excluding patients with biallelic MUTYH mutations) since introducing multi-gene panel testing in 2014. The most common second mutation was the I1307K variant in the APC gene at 20% (14/70). We also identified 20 patients who would have received incomplete genetic risk assessment if they only underwent single site testing and screening management changed in 60% (12/20) of these patients. 35% (7/20) of these patients did not meet NCCN criteria for additional germline testing beyond single site testing. Conclusions: Multi-gene hereditary cancer panels identify patients and families with multiple germline mutations. Patients undergoing single site cascade testing are at risk of receiving inaccurate risk assessment based on incomplete ascertainment of germline cancer risks. Detection of additional actionable mutations will frequently lead to changes in medical management.

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Cuperlovic-Culf, Miroslava, Nabil Belacel, Michelle Davey, and Rodney J. Ouellette. "Multi-gene biomarker panel for reference free prostate cancer diagnosis: determination and independent validation." Biomarkers 15, no. 8 (October 2010): 693–706. http://dx.doi.org/10.3109/1354750x.2010.511268.

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47

Guindalini, Rodrigo Santa Cruz, Danilo Viana, João Paulo Kitajima, Andre Valim, David Schlesinger, Fernando Kok, and Maria A. A. Koike Folgueira. "Detection of inherited mutations in Brazilian breast cancer patients using multi-gene panel testing." Journal of Clinical Oncology 36, no. 15_suppl (May 20, 2018): e13610-e13610. http://dx.doi.org/10.1200/jco.2018.36.15_suppl.e13610.

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48

Pritzlaff, Mary, Pia Summerour, Rachel McFarland, Shuwei Li, Patrick Reineke, Jill S. Dolinsky, David E. Goldgar, et al. "Male breast cancer in a multi-gene panel testing cohort: insights and unexpected results." Breast Cancer Research and Treatment 161, no. 3 (December 22, 2016): 575–86. http://dx.doi.org/10.1007/s10549-016-4085-4.

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Hermel, David J., Wendy C. McKinnon, Marie E. Wood, and Marc S. Greenblatt. "Multi-gene panel testing for hereditary cancer susceptibility in a rural Familial Cancer Program." Familial Cancer 16, no. 1 (July 11, 2016): 159–66. http://dx.doi.org/10.1007/s10689-016-9913-5.

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Katragadda, Shanmukh, Taryn O. Hall, Radhakrishna Bettadapura, Joline C. Dalton, Aparna Ganapathy, Pallavi Ghana, Ramesh Hariharan, et al. "Determining Cost-Optimal Next-Generation Sequencing Panels for Rare Disease and Pharmacogenomics Testing." Clinical Chemistry 67, no. 8 (June 13, 2021): 1122–32. http://dx.doi.org/10.1093/clinchem/hvab059.

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Abstract Background Multi–gene panel sequencing using next-generation sequencing (NGS) methods is a key tool for genomic medicine. However, with an estimated 140 000 genomic tests available, current system inefficiencies result in high genetic-testing costs. Reduced testing costs are needed to expand the availability of genomic medicine. One solution to improve efficiency and lower costs is to calculate the most cost-effective set of panels for a typical pattern of test requests. Methods We compiled rare diseases, associated genes, point prevalence, and test-order frequencies from a representative laboratory. We then modeled the costs of the relevant steps in the NGS process in detail. Using a simulated annealing-based optimization procedure, we determined panel sets that were more cost-optimal than whole exome sequencing (WES) or clinical exome sequencing (CES). Finally, we repeated this methodology to cost-optimize pharmacogenomics (PGx) testing. Results For rare disease testing, we show that an optimal choice of 4–6 panels, uniquely covering genes that comprise 95% of the total prevalence of monogenic diseases, saves $257–304 per sample compared with WES, and $66–135 per sample compared with CES. For PGx, we show that the optimal multipanel solution saves $6–7 (27%–40%) over a single panel covering all relevant gene–drug associations. Conclusions Laboratories can reduce costs using the proposed method to obtain and run a cost-optimal set of panels for specific test requests. In addition, payers can use this method to inform reimbursement policy.

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