Cargando…

Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population

BACKGROUND: Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple...

Descripción completa

Detalles Bibliográficos
Autores principales: Motoike, Ikuko N, Matsumoto, Mitsuyo, Danjoh, Inaho, Katsuoka, Fumiki, Kojima, Kaname, Nariai, Naoki, Sato, Yukuto, Yamaguchi-Kabata, Yumi, Ito, Shin, Kudo, Hisaaki, Nishijima, Ichiko, Nishikawa, Satoshi, Pan, Xiaoqing, Saito, Rumiko, Saito, Sakae, Saito, Tomo, Shirota, Matsuyuki, Tsuda, Kaoru, Yokozawa, Junji, Igarashi, Kazuhiko, Minegishi, Naoko, Tanabe, Osamu, Fuse, Nobuo, Nagasaki, Masao, Kinoshita, Kengo, Yasuda, Jun, Yamamoto, Masayuki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138778/
https://www.ncbi.nlm.nih.gov/pubmed/25109789
http://dx.doi.org/10.1186/1471-2164-15-673
Descripción
Sumario:BACKGROUND: Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. RESULTS: Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. CONCLUSIONS: Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-673) contains supplementary material, which is available to authorized users.