Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.
Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.
复制标题
DOI：
10.1038/ng.3119
复制
发表时间：
2014-12
期刊：
影响因子：
30.8
通讯作者：
Steemers, Frank J.
中科院分区：
文献类型：
--
作者：
Amini, Sasan;Pushkarev, Dmitry;Christiansen, Lena;Kostem, Emrah;Royce, Tom;Turk, Casey;Pignatelli, Natasha;Adey, Andrew;Kitzman, Jacob O.;Vijayan, Kandaswamy;Ronaghi, Mostafa;Shendure, Jay;Gunderson, Kevin L.;Steemers, Frank J.
Haplotype-resolved genomes equencing enables accurate interpretation of medically relevant genetic variation, deep inferences regarding population history, and the non-invasive prediction of fetal genomes. We describe an approach for genome-wide haplotyping based on contiguity preserving transposition (CPT-Seq) and combinatorial indexing. Tn5 transposition is used to modify DNA with adapter and index sequences while preserving contiguity. After dilution and compartmentalization, the transposase is removed, resolving the DNA into individually indexed libraries. The libraries in each compartment, enriched for neighboring genomic elements, are further indexed via PCR. Combinatorial 96-plex indexing at both the transposition and PCR stage enables the construction of phased synthetic reads from each of the nearly 10,000 “virtual compartments”. We demonstrate feasibility of this method by assembling >95% of heterozygous variants in a human genome into long, accurate haplotype blocks (N50 = 1.4–2.3 Mb). The rapid, scalable, and cost-effective workflow could enable haplotype resolution to become routine in human genome sequencing.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btq411
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Geraci F
通讯作者：
Geraci F
影响因子：
64.8
作者：
Peters, Brock A.;Kermani, Bahram G.;Sparks, Andrew B.;Alferov, Oleg;Hong, Peter;Alexeev, Andrei;Jiang, Yuan;Dahl, Fredrik;Tang, Y. Tom;Haas, Juergen;Robasky, Kimberly;Zaranek, Alexander Wait;Lee, Je-Hyuk;Ball, Madeleine Price;Peterson, Joseph E.;Perazich, Helena;Yeung, George;Liu, Jia;Chen, Linsu;Kennemer, Michael I.;Pothuraju, Kaliprasad;Konvicka, Karel;Tsoupko-Sitnikov, Mike;Pant, Krishna P.;Ebert, Jessica C.;Nilsen, Geoffrey B.;Baccash, Jonathan;Halpern, Aaron L.;Church, George M.;Drmanac, Radoje
通讯作者：
Drmanac, Radoje
DOI：
10.1073/pnas.1218696110
发表时间：
2013-04-02
影响因子：
11.1
作者：
Kaper, Fiona;Swamy, Sajani;Fan, Jian-Bing
通讯作者：
Fan, Jian-Bing
DOI：
10.1093/bioinformatics/btq215
发表时间：
2010-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
He D;Choi A;Pipatsrisawat K;Darwiche A;Eskin E
通讯作者：
Eskin E
影响因子：
7
作者：
Bansal, Vikas;Halpern, Aaron L.;Bafna, Vineet
通讯作者：
Bafna, Vineet