Tags

Type your tag names separated by a space and hit enter

A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies.
Hum Mutat. 2013 Dec; 34(12):1715-20.HM

Abstract

Accurate genotyping is important for genetic testing. Sanger sequencing-based typing is the gold standard for genotyping, but it has been underused, due to its high cost and low throughput. In contrast, short-read sequencing provides inexpensive and high-throughput sequencing, holding great promise for reaching the goal of cost-effective and high-throughput genotyping. However, the short-read length and the paucity of appropriate genotyping methods, pose a major challenge. Here, we present RCHSBT-reliable, cost-effective and high-throughput sequence based typing pipeline-which takes short sequence reads as input, but uses a unique variant calling, haploid sequence assembling algorithm, can accurately genotype with greater effective length per amplicon than even Sanger sequencing reads. The RCHSBT method was tested for the human MHC loci HLA-A, HLA-B, HLA-C, HLA-DQB1, and HLA-DRB1, upon 96 samples using Illumina PE 150 reads. Amplicons as long as 950 bp were readily genotyped, achieving 100% typing concordance between RCHSBT-called genotypes and genotypes previously called by Sanger sequence. Genotyping throughput was increased over 10 times, and cost was reduced over five times, for RCHSBT as compared with Sanger sequence genotyping. We thus demonstrate RCHSBT to be a genotyping method comparable to Sanger sequencing-based typing in quality, while being more cost-effective, and higher throughput.

Authors+Show Affiliations

BGI-Shenzhen, Shenzhen, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24014314

Citation

Cao, Hongzhi, et al. "A Short-read Multiplex Sequencing Method for Reliable, Cost-effective and High-throughput Genotyping in Large-scale Studies." Human Mutation, vol. 34, no. 12, 2013, pp. 1715-20.
Cao H, Wang Y, Zhang W, et al. A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies. Hum Mutat. 2013;34(12):1715-20.
Cao, H., Wang, Y., Zhang, W., Chai, X., Zhang, X., Chen, S., Yang, F., Zhang, C., Guo, Y., Liu, Y., Tang, Z., Chen, C., Xue, Y., Zhen, H., Xu, Y., Rao, B., Liu, T., Zhao, M., Zhang, W., ... Li, J. (2013). A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies. Human Mutation, 34(12), 1715-20. https://doi.org/10.1002/humu.22439
Cao H, et al. A Short-read Multiplex Sequencing Method for Reliable, Cost-effective and High-throughput Genotyping in Large-scale Studies. Hum Mutat. 2013;34(12):1715-20. PubMed PMID: 24014314.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies. AU - Cao,Hongzhi, AU - Wang,Yu, AU - Zhang,Wei, AU - Chai,Xianghua, AU - Zhang,Xiandong, AU - Chen,Shiping, AU - Yang,Fan, AU - Zhang,Caifen, AU - Guo,Yulai, AU - Liu,Ying, AU - Tang,Zhoubiao, AU - Chen,Caifen, AU - Xue,Yaxin, AU - Zhen,Hefu, AU - Xu,Yinyin, AU - Rao,Bin, AU - Liu,Tao, AU - Zhao,Meiru, AU - Zhang,Wenwei, AU - Li,Yingrui, AU - Zhang,Xiuqing, AU - Tellier,Laurent C A M, AU - Krogh,Anders, AU - Kristiansen,Karsten, AU - Wang,Jun, AU - Li,Jian, Y1 - 2013/10/07/ PY - 2013/04/17/received PY - 2013/08/29/accepted PY - 2013/9/10/entrez PY - 2013/9/10/pubmed PY - 2014/6/17/medline KW - HLA KW - genotyping KW - high-throughput KW - short-read next-generation sequencing SP - 1715 EP - 20 JF - Human mutation JO - Hum. Mutat. VL - 34 IS - 12 N2 - Accurate genotyping is important for genetic testing. Sanger sequencing-based typing is the gold standard for genotyping, but it has been underused, due to its high cost and low throughput. In contrast, short-read sequencing provides inexpensive and high-throughput sequencing, holding great promise for reaching the goal of cost-effective and high-throughput genotyping. However, the short-read length and the paucity of appropriate genotyping methods, pose a major challenge. Here, we present RCHSBT-reliable, cost-effective and high-throughput sequence based typing pipeline-which takes short sequence reads as input, but uses a unique variant calling, haploid sequence assembling algorithm, can accurately genotype with greater effective length per amplicon than even Sanger sequencing reads. The RCHSBT method was tested for the human MHC loci HLA-A, HLA-B, HLA-C, HLA-DQB1, and HLA-DRB1, upon 96 samples using Illumina PE 150 reads. Amplicons as long as 950 bp were readily genotyped, achieving 100% typing concordance between RCHSBT-called genotypes and genotypes previously called by Sanger sequence. Genotyping throughput was increased over 10 times, and cost was reduced over five times, for RCHSBT as compared with Sanger sequence genotyping. We thus demonstrate RCHSBT to be a genotyping method comparable to Sanger sequencing-based typing in quality, while being more cost-effective, and higher throughput. SN - 1098-1004 UR - https://www.unboundmedicine.com/medline/citation/24014314/A_short_read_multiplex_sequencing_method_for_reliable_cost_effective_and_high_throughput_genotyping_in_large_scale_studies_ L2 - https://doi.org/10.1002/humu.22439 DB - PRIME DP - Unbound Medicine ER -