Dense and accurate whole-chromosome haplotyping of individual genomes.
Dense and accurate whole-chromosome haplotyping of individual genomes.
复制标题
DOI：
10.1038/s41467-017-01389-4
复制
发表时间：
2017-11-03
影响因子：
16.6
通讯作者：
Marschall T
中科院分区：
文献类型：
--
作者：
Porubsky D;Garg S;Sanders AD;Korbel JO;Guryev V;Lansdorp PM;Marschall T
The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy that combines global, but sparse haplotypes obtained from strand-specific single-cell sequencing (Strand-seq) with dense, yet local, haplotype information available through long-read or linked-read sequencing. We provide comprehensive guidance on the required sequencing depths and reliably assign more than 95% of alleles (NA12878) to their parental haplotypes using as few as 10 Strand-seq libraries in combination with 10-fold coverage PacBio data or, alternatively, 10X Genomics linked-read sequencing data. We conclude that the combination of Strand-seq with different technologies represents an attractive solution to chart the genetic variation of diploid genomes. Haplotype information is important in investigating many biological phenomena. Here, Porubsky et al. combine Strand-seq with long-read or linked-read sequencing to obtain complete and genome-wide haplotypes of a single individual genome at manageable costs.
登录
查看更多内容
影响因子：
7
作者：
Porubský D;Sanders AD;van Wietmarschen N;Falconer E;Hills M;Spierings DC;Bevova MR;Guryev V;Lansdorp PM
通讯作者：
Lansdorp PM
影响因子：
64.5
作者：
Hnisz D;Abraham BJ;Lee TI;Lau A;Saint-André V;Sigova AA;Hoke HA;Young RA
通讯作者：
Young RA
影响因子：
1.7
作者：
Patterson, Murray;Marschall, Tobias;Schonhuth, Alexander
通讯作者：
Schonhuth, Alexander
影响因子：
46.9
作者：
de Vree, Paula J. P.;de Wit, Elzo;de Laat, Wouter
通讯作者：
de Laat, Wouter
影响因子：
7
作者：
Eberle, Michael A.;Fritzilas, Epameinondas;Bentley, David R.
通讯作者：
Bentley, David R.