On the design of clone-based haplotyping.
On the design of clone-based haplotyping.
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DOI：
10.1186/gb-2013-14-9-r100
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发表时间：
2013
期刊：
影响因子：
12.3
通讯作者：
Zhang K
中科院分区：
文献类型：
--
作者：
Lo C;Liu R;Lee J;Robasky K;Byrne S;Lucchesi C;Aach J;Church G;Bafna V;Zhang K
Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable yields due to incompletely understood parameter choices. We parameterize the clone-based haplotyping problem in order to provide theoretical and empirical assessments of the impact of different parameters on haplotype assembly. We confirm the intuition that long clones help link together heterozygous variants and thus improve haplotype length. Furthermore, given the length of the clones, we address how to choose the other parameters, including number of pools, clone coverage and sequencing coverage, so as to maximize haplotype length. We model the problem theoretically and show empirically the benefits of using larger clones with moderate number of pools and sequencing coverage. In particular, using 140 kb BAC clones, we construct haplotypes for a personal genome and assemble haplotypes with N50 values greater than 2.6 Mb. These assembled haplotypes are longer and at least as accurate as haplotypes of existing clone-based strategies, whether in vivo or in vitro. Our results provide practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes.
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影响因子：
7.7
作者：
Voskoboynik A;Neff NF;Sahoo D;Newman AM;Pushkarev D;Koh W;Passarelli B;Fan HC;Mantalas GL;Palmeri KJ;Ishizuka KJ;Gissi C;Griggio F;Ben-Shlomo R;Corey DM;Penland L;White RA 3rd;Weissman IL;Quake SR
通讯作者：
Quake SR
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.1016725108
发表时间：
2011-01-04
影响因子：
11.1
作者：
Yang, Hong;Chen, Xi;Wong, Wing Hung
通讯作者：
Wong, Wing Hung
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
影响因子：
2.1
作者：
Li, Yun;Willer, Cristen J.;Ding, Jun;Scheet, Paul;Abecasis, Goncalo R.
通讯作者：
Abecasis, Goncalo R.