Validation of novel forensic DNA markers using multiplex microhaplotype sequencing.
Validation of novel forensic DNA markers using multiplex microhaplotype sequencing.
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DOI：
10.1016/j.fsigen.2020.102275
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发表时间：
2020-07
影响因子：
3.1
通讯作者：
Scharfe, Curt
中科院分区：
文献类型：
--
作者：
Gandotra, Neeru;Speed, William C.;Qin, Wenyi;Tang, Yishuo;Pakstis, Andrew J.;Kidd, Kenneth K.;Scharfe, Curt
微单倍型（Microhaplotypes， MH）由位于基因组序列300个碱基内的多个单核苷酸多态性（snp）组成。需要改进的工具来促进微单倍型在不同人群和法医环境中的广泛应用。我们设计了一种检测90个微单倍型（mMHseq）的多重测序方法，其中包括先前研究中具有高有效等位基因数（Ae）的46个MH位点，以及从1000基因组（1KG）项目中鉴定出的含有4至14个snp的44个高Ae MH位点。mMHseq的独特设计集成了一种从少量DNA中进行多重扩增的新方法，并在一次MiSeq中对48个样品进行多重测序，以检测所有相关的MH变异。在来自非洲、亚洲和欧洲7个不同世界种群的156个个体的队列中评估了检测性能。其中三个来自东非的种群（Chagga， Sandawe和Zaramo）和一个来自东欧的种群（Adygei）有足够的个体测序，可以纳入26个1KG种群的统计分析。30个种群的全球平均Ae为5.08（范围：2.7 ~ 11.54），平均生物地理变异信息性（In）为0.30（范围：0.08 ~ 0.70）。在90个微单倍型中的58个中检测到85个新的snp。开发了基于网络的开源软件，用于可视化每个微单倍型和个体的单倍型阶段数据。我们的多重微单倍型测序方法可以根据新基因座的发现进行定制和扩展。
Microhaplotypes (MH) are comprised of multiple single nucleotide polymorphisms (SNPs) that are located within 300 bases of genomic sequence. Improved tools are needed to facilitate broader application of microhaplotypes in a diverse range of populations and forensic settings. We designed an assay for multiplex sequencing of 90 microhaplotypes (mMHseq) that include 46 MH loci with high Effective Number of Alleles (Ae) from previous studies, and 44 high Ae MH loci containing between four to fourteen SNPs that were identified from the 1000 Genomes (1KG) Project. The unique design of mMHseq integrates a novel method for multiplex amplification from small DNA amounts, and multiplex sequencing of 48 samples in a single MiSeq run to detect all relevant MH variation. Assay performance was evaluated in a cohort of 156 individuals from seven different world populations from Africa, Asia, and Europe. Three of those populations from East Africa (Chagga, Sandawe, and Zaramo) and one from Eastern Europe (Adygei) had sufficient individuals sequenced by the assay to be included in statistical analyses with the 26 1KG populations. For those 30 populations the mean global average Ae was 5.08 (range: 2.7–11.54) and mean informativeness for biogeographic variation (In) was 0.30 (range: 0.08-0.70). Eighty-five novel SNPs were detected in 58 of the 90 microhaplotypes. Open-source, web-based software was developed to visualize haplotype phase data for each microhaplotype and individual. Our approach for multiplex microhaplotype sequencing can be customized and expanded as novel loci are being discovered.
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影响因子：
3.1
作者：
de la Puente, M.;Phillips, C.;Lareu, M., V
通讯作者：
Lareu, M., V
DOI：
10.1186/s13323-014-0018-3
发表时间：
2015
期刊：
Investigative genetics
影响因子：
--
作者：
Kidd KK;Speed WC
通讯作者：
Speed WC
DOI：
10.1016/j.fsigss.2017.09.209
发表时间：
2017-12-01
期刊：
FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES
影响因子：
--
作者：
Oldoni, Fabio;Hart, Rebecca;Podini, Daniele
通讯作者：
Podini, Daniele
影响因子：
3.1
作者：
Kidd, Kenneth K.;Speed, William C.;Soundararajan, Usha
通讯作者：
Soundararajan, Usha
影响因子：
2.1
作者：
Bulbul O;Pakstis AJ;Soundararajan U;Gurkan C;Brissenden JE;Roscoe JM;Evsanaa B;Togtokh A;Paschou P;Grigorenko EL;Gurwitz D;Wootton S;Lagace R;Chang J;Speed WC;Kidd KK
通讯作者：
Kidd KK