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Journal articles on the topic 'Sanger'

Author: Grafiati
Published: 4 June 2021
Last updated: 30 July 2024

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1

Lagnado, John. "Fred Sanger." Biochemist 27, no. 6 (December 1, 2005): 37–39. http://dx.doi.org/10.1042/bio02706037.

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2

Yasunari, Kristie. "Margaret Sanger." Peace Review 12, no. 4 (December 2000): 619–26. http://dx.doi.org/10.1080/10402650020014735.

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3

Tippett, P. "Ruth Sanger." Vox Sanguinis 81, no. 4 (November 2001): 211–12. http://dx.doi.org/10.1046/j.1423-0410.2001.00121.x.

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4

Watts, Geoff. "Frederick Sanger." Lancet 382, no. 9908 (December 2013): 1872. http://dx.doi.org/10.1016/s0140-6736(13)62614-8.

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5

Estrada-Rivadeneyra, Diego. "Sanger sequencing." FEBS Journal 284, no. 24 (November 24, 2017): 4174. http://dx.doi.org/10.1111/febs.14319.

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6

Mollison, Patrick L. "Ruth Sanger." Transfusion 42, no. 1 (January 2002): 125–26. http://dx.doi.org/10.1046/j.1537-2995.2002.00054.x.

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7

Tack, Jan. "Response to Sanger." American Journal of Gastroenterology 109, no. 3 (March 2014): 445–46. http://dx.doi.org/10.1038/ajg.2014.17.

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8

Davies, Martin J. "Celera vs Sanger." Trends in Biotechnology 19, no. 3 (March 2001): 88. http://dx.doi.org/10.1016/s0167-7799(01)01588-8.

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9

Dodson, Guy. "Fred Sanger: sequencing pioneer." Biochemist 27, no. 6 (December 1, 2005): 31–35. http://dx.doi.org/10.1042/bio02706031.

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Fred Sanger is a biochemist who practised chemistry and whose discoveries have been fundamental to the development of modern biological science. His insights into sequencing methods and the central roles played by proteins and nucleic acids in the molecular processes of biology led him to dedicate a lifetime to their investigation. Together with his shrewd chemical judgement, his experimental skill and his tenacity, this made him one of the most productive and remarkable biochemists of our time.
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10

Brenner, S. "Frederick Sanger (1918-2013)." Science 343, no. 6168 (January 16, 2014): 262. http://dx.doi.org/10.1126/science.1249912.

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11

Mikulski, Matthew. "Pushing the Sanger envelope." Science-Business eXchange 1, no. 1 (January 2008): 5. http://dx.doi.org/10.1038/scibx.2008.5.

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12

Brownlee, George G. "Frederick Sanger (1918–2013)." Current Biology 23, no. 24 (December 2013): R1074—R1076. http://dx.doi.org/10.1016/j.cub.2013.11.037.

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13

Carpente, Luisa, Ana Cerdeira-Pena, Silvia Lorenzo-Freire, and Ángeles S. Places. "Optimization in Sanger sequencing." Computers & Operations Research 109 (September 2019): 250–62. http://dx.doi.org/10.1016/j.cor.2019.05.011.

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14

Walker, John. "Frederick Sanger (1918–2013)." Nature 505, no. 7481 (January 2014): 27. http://dx.doi.org/10.1038/505027a.

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15

Sanger, Frkderick. "Wer ist's? - Frederick Sanger." Nachrichten aus Chemie und Technik 6, no. 22-23 (April 24, 2010): 331. http://dx.doi.org/10.1002/nadc.19580062203.

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16

Coulson, Alan. "Frederick Sanger (1918-2013)." Angewandte Chemie 126, no. 12 (February 3, 2014): 3120. http://dx.doi.org/10.1002/ange.201310781.

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17

Coulson, Alan. "Frederick Sanger (1918-2013)." Angewandte Chemie International Edition 53, no. 12 (February 3, 2014): 3060. http://dx.doi.org/10.1002/anie.201310781.

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18

Chen, Cen, Bingguo Lu, Xiaofang Huang, Chuyun Bi, Lili Zhao, Yunzhuo Hu, Xuanyang Chen, Shiqiang Lin, and Kai Huang. "A Python script to merge Sanger sequences." PeerJ 9 (April 27, 2021): e11354. http://dx.doi.org/10.7717/peerj.11354.

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Merging Sanger sequences is frequently needed during the gene cloning process. In this study, we provide a Python script that is able to assemble multiple overlapping Sanger sequences. The script utilizes the overlapping regions within the tandem Sanger sequences to merge the Sanger sequences. The results demonstrate that the script can produce the merged sequence from the input Sanger sequences in a single run. The script offers a simple and free method for merging Sanger sequences and is useful for gene cloning.
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19

Moskowitz, Eva, Barbara Abrash, Terese Svoboda, and Steve Bull. "Margaret Sanger: A Public Nuisance." American Historical Review 98, no. 4 (October 1993): 1179. http://dx.doi.org/10.2307/2166615.

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20

Valenza, Charles. "Was Margaret Sanger a Racist?" Family Planning Perspectives 17, no. 1 (January 1985): 44. http://dx.doi.org/10.2307/2135230.

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21

Duffin, Christian. "The Wellcome Trust Sanger Institute." Nursing Standard 29, no. 22 (January 28, 2015): 30. http://dx.doi.org/10.7748/ns.29.22.30.s35.

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22

Morantz-Sanchez, Regina, and Babara Abrash. "Margaret Sanger: A Public Nuisance." Journal of American History 82, no. 3 (December 1995): 1317. http://dx.doi.org/10.2307/2945288.

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23

Tollefson, Gary D., and Todd M. Sanger. "Drs. Tollefson and Sanger Reply." American Journal of Psychiatry 155, no. 8 (August 1998): 1133–11334. http://dx.doi.org/10.1176/ajp.155.8.1133.

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24

Berg, P. "Fred Sanger: A memorial tribute." Proceedings of the National Academy of Sciences 111, no. 3 (January 21, 2014): 883–84. http://dx.doi.org/10.1073/pnas.1323264111.

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25

Berkman, Joyce. "The Question of Margaret Sanger." History Compass 9, no. 6 (June 2011): 474–84. http://dx.doi.org/10.1111/j.1478-0542.2011.00769.x.

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26

Myskja, Audun. "Sanger om fortvilelse og håp." Tidsskrift for Den norske legeforening 136, no. 5 (2016): 457. http://dx.doi.org/10.4045/tidsskr.15.1374.

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27

Wilson, Aimee Armande. "Modernism, Monsters, and Margaret Sanger." MFS Modern Fiction Studies 59, no. 2 (2013): 440–60. http://dx.doi.org/10.1353/mfs.2013.0027.

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28

Stevens, Hallam. "Dr. Sanger, meet Mr. Moore." BioEssays 34, no. 2 (November 2, 2011): 103–5. http://dx.doi.org/10.1002/bies.201100146.

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29

ㅤ. "Peeters / Sanger (TvAR 1998/4924)." Tijdschrift voor Agrarisch Recht 58, no. 7 (July 1, 1998): ㅤ. http://dx.doi.org/10.5117/tvar1998.7-8.002.

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30

Zeng, Xiaofang, Tianyu Lian, Jianhui Lin, Suqi Li, Haikuo Zheng, Chunyan Cheng, Jue Ye, Zhicheng Jing, Xiaojian Wang, and Wei Huang. "Whole-exome sequencing improves genetic testing accuracy in pulmonary artery hypertension." Pulmonary Circulation 8, no. 2 (February 26, 2018): 204589401876368. http://dx.doi.org/10.1177/2045894018763682.

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Sanger sequencing, the traditional “gold standard” for mutation detection, has been wildly used in genetic testing of pulmonary artery hypertension (PAH). However, with the advent of whole-exome sequencing (WES), few studies have compared the accuracy of WES and Sanger sequencing in routine genetic testing of PAH. PAH individuals were enrolled from Fu Wai Hospital and Shanghai Pulmonary Hospital. WES was used to analyze DNA samples from 120 PAH patients whose bone morphogenetic protein receptor type 2 (BMPR2) mutation statuses had been previously studied using Sanger sequencing. The Sanger sequencing and WES agreement was 98.3% (118/120) with near-perfect agreement (κ coefficient = 0.848). There was no significant difference between the two methods on the McNemar–Bowker test ( P > 0.05). Twenty-one BMPR2 mutation carriers and 99 non-carriers were detected by Sanger sequencing. Among the 21 BMPR2 carriers detected by Sanger sequencing, one variant (c.1040 T > A) was not found by WES. Among the 99 BMPR2 non-carriers, WES detected an extra mutation carrier (c.76 + 1 G > C) missed by Sanger sequencing. Both false-positive and false-negative results were highly conserved and were re-analyzed by Sanger sequencing. WES improved the accuracy of Sanger sequencing and detected 1% (1/99) false-positive and 4.8% (1/21) false-negative results of Sanger sequencing. No false-positive and false-negative results of WES were identified in our analysis. WES is non-inferior to Sanger sequencing and may play a more important role in genetic testing of PAH patients in the future.
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31

Beck, Tyler F., James C. Mullikin, and Leslie G. Biesecker. "Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants." Clinical Chemistry 62, no. 4 (April 1, 2016): 647–54. http://dx.doi.org/10.1373/clinchem.2015.249623.

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Abstract BACKGROUND Next-generation sequencing (NGS) data are used for both clinical care and clinical research. DNA sequence variants identified using NGS are often returned to patients/participants as part of clinical or research protocols. The current standard of care is to validate NGS variants using Sanger sequencing, which is costly and time-consuming. METHODS We performed a large-scale, systematic evaluation of Sanger-based validation of NGS variants using data from the ClinSeq® project. We first used NGS data from 19 genes in 5 participants, comparing them to high-throughput Sanger sequencing results on the same samples, and found no discrepancies among 234 NGS variants. We then compared NGS variants in 5 genes from 684 participants against data from Sanger sequencing. RESULTS Of over 5800 NGS-derived variants, 19 were not validated by Sanger data. Using newly designed sequencing primers, Sanger sequencing confirmed 17 of the NGS variants, and the remaining 2 variants had low quality scores from exome sequencing. Overall, we measured a validation rate of 99.965% for NGS variants using Sanger sequencing, which was higher than many existing medical tests that do not necessitate orthogonal validation. CONCLUSIONS A single round of Sanger sequencing is more likely to incorrectly refute a true-positive variant from NGS than to correctly identify a false-positive variant from NGS. Validation of NGS-derived variants using Sanger sequencing has limited utility, and best practice standards should not include routine orthogonal Sanger validation of NGS variants.
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32

Tampilang, Yulicia, Theresye Wantania, and Susan Monoarfa. "CAMPUR KODE BAHASA SANGER DIALEK SIAU DALAM PENGGUNAAN BAHASA INDONESIA DI DESA BUHIAS KECAMATAN SIAU TIMUR SELATAN." KOMPETENSI 2, no. 10 (December 23, 2022): 1743–51. http://dx.doi.org/10.53682/kompetensi.v2i10.4761.

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Tujuan penelitian ini ialah untuk mendeskripsikan campur kode bahasa sanger dialek siau dalam penggunaan Bahasa Indonesia di Desa Buhias Kecamatan Siau Timur Selatan Kabupaten Siau Tagulandang Biaro. Metode yang digunakan dalam penelitian ini adalah metode deskriptif kualitatif. Sumber data penelitian adalah informan bahasa Sanger dialek Siau yang berdomisili di desa Buhias Kecamatan Siau Timur Selatan. Untuk mengumpulkan data, teknik yang digunakan adalah teknik rekam, teknik catat, teknik simak.Hasil penelitian menunjukkan bahwa : 1) Campur kode dalam bentuk kata bahasa Sanger dialek Siau dalam penggunaan bahasa Indonesia adalah 71,44% campur kode dalam bentuk frasa bahasa Sanger dialek Siau dalam penggunaan bahasa Indonesia adalah 28,55%. 2) Dari segi bentuk tuturan (1) aparat desa bercampur kode kata bahasa Sanger dialek Siau 33,33 % dan frasa 66,66 % dalam penggunaan bahasa Indonesia. Pada tuturan (2) ibu-ibu rumah tangga bercampur kode kata bahasa Sanger dialek Siau 73,33 % dan frasa 26,66 % dalam penggunaan bahasa Indonesia. Pada tuturan (3) aparat desa dan masyarakat bercampur kode kata bahasa Sanger dialek Siau 81,25 % dan frasa 18,75 % dalam penggunaan bahasa Indonesia. Pada tuturan (4) Ibu-ibu rumah tangga bercampur kode kata bahasa Sanger dialek Siau 81,81 % dan frasa 18,18 % dalam penggunaan bahasa Indonesia. (5) Remaja bercampur kode kata bahasa Sanger dialek Siau 87,5 % dan frasa 12,5 % dalam penggunaan bahasa Indonesia. 3) Dari segi makna tuturan memuat tindak tutur mengundang, memuat tindak tutur menyatakan, memuat ajakan, memuat tindak tutur bertanya.
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33

Lu, Sang-Yu, Ying-Chao Chen, Jia-Lin Feng, Qin-Yi Zhou, Jing Chen, Chen-Fang Zhu, Miao-Miao Guo, et al. "Detection of BRAF V600E in Fine-Needle Aspiration Samples of Thyroid Nodules by Droplet Digital PCR." International Journal of Endocrinology 2022 (March 29, 2022): 1–8. http://dx.doi.org/10.1155/2022/6243696.

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Background. BRAF exon 15 p.V600E (BRAF V600E) mutation has been established as an important molecular marker for papillary thyroid carcinoma diagnosis by ultrasound-guided fine-needle aspiration biopsy (FNAB). Sanger sequencing is the gold standard for detecting BRAF V600E mutations but fails to identify low-frequency mutations. However, droplet digital PCR (ddPCR) is a popular new method for detecting low-frequency mutations. Here, we compare the efficiency of droplet digital PCR (ddPCR) and Sanger sequencing for detection of the BRAF V600E mutation in thyroid fine-needle aspiration (FNA) samples. Methods. Thyroid fine-needle aspiration samples from 278 patients with 310 thyroid nodules were collected. Sanger sequencing and ddPCR were conducted to detect the BRAF V600E mutation. Results. The BRAF V600E mutation was found in 94 nodules (30.32%) by ddPCR and 40 nodules (12.90%) by Sanger sequencing in 310 FNA samples. A total of 119 nodules were confirmed PTC by postsurgical pathology. Among which the BRAF mutation was found in 80 (67.23%) nodules by ddPCR and 31 (26.05%) by Sanger sequencing. All nodules carrying the mutation detected by Sanger sequencing (SS+) were verified by ddPCR (ddPCR+). Also, all nodules with no mutation detected by ddPCR were interpreted as wild-type by Sanger sequencing (SS−). In addition. Almost all SS+/ddPCR + nodules (95.00%; 38/40) and SS−/ddPCR + nodules (100.00%; 54/54) displayed a BRAF mutation rate of >5% and <15%, respectively, indicating easy misdetection by Sanger sequencing when the mutation rate is between 5 and 15%. Conclusion. ddPCR has higher sensitivity than Sanger sequencing and we propose ddPCR as a supplement to Sanger sequencing in molecular testing of BRAF using FNAB samples.
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34

Zhang, Man-San, Yi-Chen Yeh, Hsien-Neng Huang, Long-Wei Lin, Yen-Lin Huang, Lei-Chi Wang, Lai-Jin Yao, et al. "The association of EGFR amplification with aberrant exon 20 insertion report using the cobas EGFR Mutation Test v2." PLOS ONE 19, no. 4 (April 30, 2024): e0301120. http://dx.doi.org/10.1371/journal.pone.0301120.

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Determining the exact type of epidermal growth factor receptor (EGFR) exon 20 insertion (ex20ins) mutation in lung cancer has become important. We found that not all ex20ins mutations reported by cobas EGFR test v2 could be validated by Sanger sequencing even using surgical specimens with high tumor contents. This study aimed to validate the ex20ins results reported by the cobas test and to determine whether there were clinicopathological factors associated with aberrant cobas ex20ins report. In total, 123 cobas-reported cases with ex20ins were retrospectively collected and validated by Sanger sequencing and Idylla assay. Clinicopathological features between ex20ins cobas+/Sanger+ group (n = 71) and cobas+/Sanger− group (n = 52) were compared. The Idylla assay detected ex20ins in 82.6% of cobas+/Sanger+ cases but only in 4.9% of cobas+/Sanger− cases. The cobas+/Sanger− group was significantly associated with higher tumor contents, poorly differentiated patterns, tumor necrosis, and a lower internal control cycle threshold value reported by the Idylla which suggesting the presence of increased EGFR gene copy numbers. EGFR fluorescence in situ hybridization (FISH) revealed the majority of cobas+/Sanger− group had EGFR high copy number gain (16%) or amplification (76%) according to the Colorado criteria. Among cases reported to have concomitant classic EGFR and ex20ins mutations by the cobas, the classic EGFR mutations were all detected by Sanger sequencing and Idylla, while the ex20ins mutations were undetected by Sanger sequencing (0%) or rarely reported by Idylla assay (3%). FISH revealed high EGFR copy number gain (17.9%) and amplification (79.5%) in cases reported having concomitant classic EGFR and ex20ins mutations by the cobas. This study demonstrated an unusually high frequency of EGFR amplification in cases with aberrant cobas ex20ins report which could not be validated by Sanger sequencing or Idylla assay. Ex20ins reported by the cobas test should be validated using other methods especially those reported having concomitant ex20ins and classic EGFR mutations.
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35

Fields, Stanley. "Would Fred Sanger Get Funded Today?" Genetics 197, no. 2 (June 2014): 435–39. http://dx.doi.org/10.1534/genetics.114.165134.

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36

Phelps, Christopher. "Margaret Sanger, “The Unrecorded Battle” (1912)." Labor 19, no. 1 (March 1, 2022): 165–74. http://dx.doi.org/10.1215/15476715-9475817.

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37

Vogel, G. "GENOMICS: Sanger Will Sequence Zebrafish Genome." Science 290, no. 5497 (December 1, 2000): 1671b—1671. http://dx.doi.org/10.1126/science.290.5497.1671b.

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38

Singh, Vivek. "In memoriam : Frederick Sanger (1918-2013)." International Journal of Applied Sciences and Biotechnology 1, no. 4 (December 21, 2013): 158–61. http://dx.doi.org/10.3126/ijasbt.v1i4.9313.

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39

Meyer, J. W. "Margaret Sanger: A Life of Passion." Journal of American History 99, no. 2 (August 20, 2012): 627–28. http://dx.doi.org/10.1093/jahist/jas266.

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40

Aldridge, Susan. "Sanger Institute looks to the future." Genome Biology 2 (2001): spotlight—20011106–02. http://dx.doi.org/10.1186/gb-spotlight-20011106-02.

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41

Watson, Helena. "Woman Rebel: The Margaret Sanger Story." Journal of Family Planning and Reproductive Health Care 40, no. 4 (September 19, 2014): 260. http://dx.doi.org/10.1136/jfprhc-2014-101052.

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42

Pierce, Steven R. "Ruth Sanger, a rare early photograph." Transfusion 48, no. 5 (May 2008): 799–800. http://dx.doi.org/10.1111/j.1537-2995.2008.01679.x.

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43

Hopwood, David A. "Streptomyces genes: from Waksman to Sanger." Journal of Industrial Microbiology and Biotechnology 30, no. 8 (August 1, 2003): 468–71. http://dx.doi.org/10.1007/s10295-003-0031-7.

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44

Zimmermann, J., H. Voss, C. Schwager, J. Stegemann, and W. Ansorge. "Automated Sanger dideoxy sequencing reaction protocol." FEBS Letters 233, no. 2 (June 20, 1988): 432–36. http://dx.doi.org/10.1016/0014-5793(88)80477-0.

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45

Basberg, Bjørn L. "Chesley W. Sanger, Scottish Arctic Whaling." Northern Scotland 10, no. 1 (May 2019): 100–103. http://dx.doi.org/10.3366/nor.2019.0173.

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46

Tampake, Tony, and Janhard Katampuge. "Sakralitas Kue Adat Tamo Untuk Inklusivitas Keagamaan Masyarakat di Sanger, Sulawesi Utara." Indonesian Journal of Religion and Society 4, no. 2 (December 30, 2022): 69–79. http://dx.doi.org/10.36256/ijrs.v4i2.231.

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Sanger community in North Sulawesi has one type of sacred food called Kue Adat Tamo. The food has become medium and symbol of Sanger community's religious worship. The sacredness of Tamo Traditional Cake is internalized and expressed in an annual Tulude ritual forming their inclusive social religious identity. Therefore, this paper aims to answer the ontological question about the understanding of Sanger community in Tuma towards the sacredness of Tamo Traditional Cake that becomes their collective expression and inclusiveness. To answer this question, the research was conducted using a qualitative approach and the type of ethnographic research as well as data collection techniques through interviews and observations carried out in Tuma Sanger Village. The result of the study indicates that the sacredness of Tamo Traditional Cake lies in the collective admiration and respect of Tuma community in Sanger for Ghenggonalangi which is symbolically expressed in the community's annual thanksgiving party known as Tulude. Based on these findings, the main argument of this paper is that the sacredness of Tamo Traditional Cake is rooted in the acculturation of religious culture and the social reality of Tuma Sanger community.
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47

Qu, Kevin Z., Qiulu Pan, Xi Zhang, Luis Rodriguez, Jennifer Uyeji, Hairong Li, Albert Ho, et al. "Detection of BRAF mutations in melanoma: Rate of mutation detection at codon 600 using Sanger sequencing as compared to the cobas 4800 method." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): 8596. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.8596.

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8596 Background: Detection of BRAF V600 mutations is currently a prerequisite for approved use of vemurafenib in patients with metastatic melanoma. The cobas 4800 BRAF V600 Mutation Test (Roche Molecular Diagnostics), a PCR-based assay approved to aid in selecting patients for vemurafenib therapy, primarily detects V600E. It is also reported to detect V600K, which has been associated with vemurafenib response as well. We compared the mutation detection rate of the cobas assay with that of Sanger sequencing. Methods: 125 de-identified FFPE tissues submitted for BRAF mutation analysis that all showed histologically-confirmed melanoma were tested. BRAF mutations were detected using both the cobas kit and bidirectional Sanger sequencing using BigDye kits (Applied Biosystems). DNA was extracted from 5-um sections without macrodissection using the cobas DNA extraction kit (for the cobas test) or from 5-10-um sections using Agencourt extraction kits (Beckman Coulter) following macrodissection. Results: The two methods showed agreement in 104/125 (83.2%) of cases (Table). Sanger sequencing detected V600 dinucleotide mutations in 9 samples that were negative by the cobas assay. Sanger sequencing produced no results in 10 cases owing to suboptimal PCR, including 2 that were positive by the cobas assay. The cobas assay produced 2 invalid results, including 1 that was positive for V600E by Sanger.The cobas assay detected 7/11 V600K mutations. Conclusions: Overall agreement between cobas and Sanger sequencing was 83.2%. The Sanger method had higher analytic sensitivity, resulting in nine additional V600 mutations not called by cobas compared to the two seen by cobas but not Sanger sequencing. Thus, 16% (9/57) more patients would be identified as candidates for vemurafenib therapy using the Sanger method. [Table: see text]
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48

Singh, Aditya, and Prateek Bhatia. "Automated Sanger Analysis Pipeline (ASAP): A Tool for Rapidly Analyzing Sanger Sequencing Data with Minimum User Interference." Journal of Biomolecular Techniques : JBT 27, no. 4 (December 2016): 129–31. http://dx.doi.org/10.7171/jbt.16-2704-005.

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49

Diekstra, Adinda, Ermanno Bosgoed, Alwin Rikken, Bart van Lier, Erik-Jan Kamsteeg, Marloes Tychon, Ronny C. Derks, et al. "Translating Sanger-Based Routine DNA Diagnostics into Generic Massive Parallel Ion Semiconductor Sequencing." Clinical Chemistry 61, no. 1 (January 1, 2015): 154–62. http://dx.doi.org/10.1373/clinchem.2014.225250.

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Abstract BACKGROUND Dideoxy-based chain termination sequencing developed by Sanger is the gold standard sequencing approach and allows clinical diagnostics of disorders with relatively low genetic heterogeneity. Recently, new next generation sequencing (NGS) technologies have found their way into diagnostic laboratories, enabling the sequencing of large targeted gene panels or exomes. The development of benchtop NGS instruments now allows the analysis of single genes or small gene panels, making these platforms increasingly competitive with Sanger sequencing. METHODS We developed a generic automated ion semiconductor sequencing work flow that can be used in a clinical setting and can serve as a substitute for Sanger sequencing. Standard amplicon-based enrichment remained identical to PCR for Sanger sequencing. A novel postenrichment pooling strategy was developed, limiting the number of library preparations and reducing sequencing costs up to 70% compared to Sanger sequencing. RESULTS A total of 1224 known pathogenic variants were analyzed, yielding an analytical sensitivity of 99.92% and specificity of 99.99%. In a second experiment, a total of 100 patient-derived DNA samples were analyzed using a blind analysis. The results showed an analytical sensitivity of 99.60% and specificity of 99.98%, comparable to Sanger sequencing. CONCLUSIONS Ion semiconductor sequencing can be a first choice mutation scanning technique, independent of the genes analyzed.
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Perdana, Adhitya Bayu, Asri C. Adisasmita, Rizky Ifandriani Putri, and Bayu Brahma. "BRAF V600E Mutation Test in Fine Needle Aspiration (FNA) Specimens of Thyroid Nodules by Competitive Allele-Specific TaqMan PCR (castPCR)." Indonesian Journal of Cancer 17, no. 4 (December 22, 2023): 343. http://dx.doi.org/10.33371/ijoc.v17i4.1143.

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Abstract:
Background: BRAF V600E mutation has been confirmed as a significant molecular indicator for the diagnosis and prognosis of papillary thyroid carcinoma (PTC). Sanger sequencing is the recognized approach for BRAF V600E mutation analysis, yet it is not proficient at detecting mutations that occur at low frequencies, especially in thyroid fine needle aspiration (FNA) specimens. This study aimed to evaluate the diagnostic value of Competitive Allele-Specific TaqMan PCR (castPCR) as a new reliable method for BRAF V600E mutation test in thyroid FNA specimens compared to Sanger sequencing. Methods: Thirty patients with thyroid nodules were enrolled prospectively at Dharmais Cancer Hospital Jakarta from 2013–2014. The BRAF V600E mutation was analyzed from FNA specimens using castPCR and Sanger Sequencing methods. The sensitivity and specificity of those methods were compared with routine diagnostic histopathological examination as a gold standard for PTC assessment.Results: A total of 66.6% (20/30) cases were confirmed as PTC by postsurgical histopathological examination. Among these, the BRAF V600E mutation was found in 60.0% (12/20) by castPCR and 40.0% (8/20) by Sanger sequencing. Neither castPCR nor Sanger sequencing detected BRAF V600E mutation in other nodular thyroid diseases. The sensitivity and specificity of castPCR were 60.0% and 100.0%, while Sanger sequencing was 40.0% and 100.0%, respectively. Conclusions: This study indicated that castPCR has a higher sensitivity for the BRAF V600E mutation test than Sanger Sequencing, especially in samples with a low abundance of mutant alleles. A sensitive, rapid, and easy castPCR method is reliable for evaluating BRAF V600E mutation and can improve PTC preoperative diagnosis in clinical settings.
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