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| Item Type: | Article |
|---|---|
| Title: | Multi-platform discovery of haplotype-resolved structural variation in human genomes |
| Creators Name: | Chaisson, M.J.P., Sanders, A.D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E.J., Rodriguez, O.L., Guo, L., Collins, R.L., Fan, X., Wen, J., Handsaker, R.E., Fairley, S., Kronenberg, Z.N., Kong, X., Hormozdiari, F., Lee, D., Wenger, A.M., Hastie, A.R., Antaki, D., Anantharaman, T., Audano, P.A., Brand, H., Cantsilieris, S., Cao, H., Cerveira, E., Chen, C., Chen, X., Chin, C.S., Chong, Z., Chuang, N.T., Lambert, C.C., Church, D.M., Clarke, L., Farrell, A., Flores, J., Galeev, T., Gorkin, D.U., Gujral, M., Guryev, V., Heaton, W.H., Korlach, J., Kumar, S., Kwon, J.Y., Lam, E.T., Lee, J.E., Lee, J., Lee, W.P., Lee, S.P., Li, S., Marks, P., Viaud-Martinez, K., Meiers, S., Munson, K.M., Navarro, F.C.P., Nelson, B.J., Nodzak, C., Noor, A., Kyriazopoulou-Panagiotopoulou, S., Pang, A.W.C., Qiu, Y., Rosanio, G., Ryan, M., Stütz, A., Spierings, D.C.J., Ward, A., Welch, A.E., Xiao, M., Xu, W., Zhang, C., Zhu, Q., Zheng-Bradley, X., Lowy, E., Yakneen, S., McCarroll, S., Jun, G., Ding, L., Koh, C.L., Ren, B., Flicek, P., Chen, K., Gerstein, M.B., Kwok, P.Y., Lansdorp, P.M., Marth, G.T., Sebat, J., Shi, X., Bashir, A., Ye, K., Devine, S.E., Talkowski, M.E., Mills, R.E., Marschall, T., Korbel, J.O., Eichler, E.E. and Lee, C. |
| Abstract: | The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per genome. We also discover 156 inversions per genome and 58 of the inversions intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a three to sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The methods and the dataset presented serve as a gold standard for the scientific community allowing us to make recommendations for maximizing structural variation sensitivity for future genome sequencing studies. |
| Keywords: | Algorithms, Chromosome Mapping, Genomics, Genetic Databases, Genomic Structural Variation, Haplotypes, High-Throughput Nucleotide Sequencing, Human Genome, INDEL Mutation, Whole Genome Sequencing |
| Source: | Nature Communications |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Volume: | 10 |
| Number: | 1 |
| Page Range: | 1784 |
| Date: | 16 April 2019 |
| Official Publication: | https://doi.org/10.1038/s41467-018-08148-z |
| PubMed: | View item in PubMed |
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