A Short-Read Multiplex Sequencing Method for Reliable, Cost-Effective and High-Throughput Genotyping in Large-Scale Studies

Human Mutation

Volumn 34, Issue 12, 2013, Pages 1715-1720

  Cao, Hongzhi ^a,b   Wang, Yu ^a,c   Zhang, Wei ^a   Chai, Xianghua ^a   Zhang, Xiandong ^a   Chen, Shiping ^a   Yang, Fan ^a   Zhang, Caifen ^a   Guo, Yulai ^a   Liu, Ying ^a   Tang, Zhoubiao ^a   Chen, Caifen ^a   Xue, Yaxin ^a   Zhen, Hefu ^a   Xu, Yinyin ^a   Rao, Bin ^a   Liu, Tao ^a   Zhao, Meiru ^a   Zhang, Wenwei ^a   Li, Yingrui ^a   Zhang, Xiuqing ^a   Tellier, Laurent C A M ^a,b   Krogh, Anders ^b   Kristiansen, Karsten ^b   Wang, Jun ^a,b,d,e   Li, Jian ^a,b   more..

^a BGI SHENZHEN   (China)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^d KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^e Capital Region   (Denmark)

Author keywords

Genotyping; High throughput; HLA; Short read next generation sequencing

Indexed keywords

HLA A ANTIGEN; HLA B ANTIGEN; HLA C ANTIGEN; HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN;

AMPLICON; ARTICLE; COST EFFECTIVENESS ANALYSIS; DNA SEQUENCE; GENE SEQUENCE; GENETIC SCREENING; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

GENOTYPING; HIGH-THROUGHPUT; HLA; SHORT-READ NEXT-GENERATION SEQUENCING;

COST-BENEFIT ANALYSIS; GENETIC TESTING; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HLA ANTIGENS; HUMANS; MULTIPLEX POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS;

EID: 84887615450     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22439     Document Type: Article

References (25)

1. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. 2011. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 12(11):745-755.
2. Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, Langley RJ, Zhang L, Lee CC, Schilkey FD, Sheth V, Woodward JE, et al. 2011. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 3(65):65ra4.
3. Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, Erlich HA. 2009. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 74(5):393-403.
4. Bettinotti MP, Mitsuishi Y, Bibee K, Lau M, Terasaki PI. 1997. Comprehensive method for the typing of HLA-A, B, and C alleles by direct sequencing of PCR products obtained from genomic DNA. J Immunother 20(6):425-430.
5. Carrington M, O'Brien SJ. 2003. The influence of HLA genotype on AIDS. Annu Rev Med 54:535-551.
6. Castellani C, Picci L, Tamanini A, Girardi P, Rizzotti P, Assael BM. 2009. Association between carrier screening and incidence of cystic fibrosis. JAMA 302(23):2573-2579.
7. Danzer M, Niklas N, Stabentheiner S, Hofer K, Pröll J, Stückler C, Raml E, Polin H, Gabriel C. 2013. Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics. BMC Genomics 14(1):221.
8. Danzer M, Polin H, Hofer K, Proll J, Gabriel C. 2008. Characterisation of two novel HLA alleles, HLA-Cw*0429 and HLA-DRB3*0223. Tissue Antigens 72(5):498-499.
9. Danzer M, Polin H, Proll J, Hofer K, Fae I, Fischer GF, Gabriel C. 2007. High-throughput sequence-based typing strategy for HLA-DRB1 based on real-time polymerase chain reaction. Hum Immunol 68(11):915-917.
10. Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, Pröll J. 2009. Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol 70(11):960-964.
11. Galan M, Guivier E, Caraux G, Charbonnel N, Cosson J-F. 2010. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics 11(1):296.
12. Gravitt PE, Peyton CL, Apple RJ, Wheeler CM. 1998. Genotyping of 27 human papillomavirus types by using L1 consensus PCR products by a single-hybridization, reverse line blot detection method. J Clin Microbiol 36(10):3020-3027.
13. Holcomb CL, Höglund B, Anderson MW, Blake LA, Böhme I, Egholm M, Ferriola D, Gabriel C, Gelber SE, Goodridge D, Hawbecker S, Klein R, et al. 2011. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 77(3):206-217.
14. Lank SM, Wiseman RW, Dudley DM, O'Connor DH. 2010. A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. Hum Immunol 71(10):1011-1017.
15. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760.
16. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078-2079.
17. Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18(11):1851-1858.
18. Liao C, Mo QH, Li J, Li LY, Huang YN, Hua L, Li QM, Zhang JZ, Feng Q, Zeng R, Zhong HZ, Jia SQ, et al. 2005. Carrier screening for alpha- and beta-thalassemia in pregnancy: the results of an 11-year prospective program in Guangzhou Maternal and Neonatal hospital. Prenat Diagn 25(2):163-171.
19. Metzker ML. 2009. Sequencing technologies-the next generation. Nat Rev Genet 11(1):31-46.
20. Naito H, Hayashi S, Abe K. 2001. Rapid and specific genotyping system for hepatitis B virus corresponding to six major genotypes by PCR using type-specific primers. J Clin Microbiol 39(1):362-364.
21. Napolitano C, Priori SG, Schwartz PJ, Bloise R, Ronchetti E, Nastoli J, Bottelli G, Cerrone M, Leonardi S. 2005. Genetic testing in the long QT syndrome: development and validation of an efficient approach to genotyping in clinical practice. JAMA 294(23):2975-2980
22. Ng J, Hurley CK, Baxter-Lowe LA, Chopek M, Coppo PA, Hegland J, KuKuruga D, Monos D, Rosner G, Schmeckpeper B, Yang SY, Dupont B, et al. 1993. Large-scale oligonucleotide typing for HLA-DRB1/3/4 and HLA-DQB1 is highly accurate, specific, and reliable. Tissue Antigens 42(5):473-479.
23. Odelberg SJ, Weiss RB, Hata A, White R. 1995. Template-switching during DNA synthesis by Thermus aquaticus DNA polymerase I. Nucleic Acids Res 23(11):2049-2057.
24. Voelkerding KV, Dames SA, Durtschi JD. 2009. Next-generation sequencing: from basic research to diagnostics. Clin Chem 55(4):641-658.
25. Wang C, Krishnakumar S, Wilhelmy J, Babrzadeh F, Stepanyan L, Su LF, Levinson D, Fernandez-Vina MA, Davis RW, Davis MM, Mindrinos M. 2012. High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci USA 109(22):8676-8681.