Microhaplotypes for ancestry prediction

Oldoni, Fabio; Hart, Rebecca; Long, Kelly; Maddela, Kathrina; Cisana, Selena; Schanfield, Moses S.; Wootton, Sharon; Chang, Joseph; Lagacé, Robert; Hasegawa, Ryo; Kídd, Kenneth K.; Podini, Daniele

doi:10.1016/j.fsigss.2017.09.209

Cited by 22 publications

(13 citation statements)

References 5 publications

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“…MPS technologies have many advantages in molecular forensics, and other groups have already applied them to MH analysis [7,8,[10][11][12][14][15][16][17][18][19][20]. However, establishing MPS technology in the forensic laboratory has remained a major challenge.…”

Section: Discussionmentioning

confidence: 99%

“…While MH loci can convey more information on identity and ancestry than the same number of individual SNPs [13], standardized MPS solutions for establishing MH panels are currently not commercially available. There is great enthusiasm among forensic researchers to now expand the success of SNPs and establish the next-generation of forensic markers based on multiallelic microhaplotypes [7,8,[10][11][12][14][15][16][17][18][19][20].…”

Section: Introductionmentioning

confidence: 99%

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Validation of novel forensic DNA markers using multiplex microhaplotype sequencing

Gandotra¹,

Speed²,

Qin

et al. 2020

Forensic Science International: Genetics

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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 (A e) from previous studies [1], and 44 high A e 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 A e was 5.08 (range: 2.7-11.54) and mean informativeness for biogeographic variation (I n) 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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Validation of novel forensic DNA markers using multiplex microhaplotype sequencing

Gandotra¹,

Speed²,

Qin

et al. 2020

Forensic Science International: Genetics

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“…Based on these characteristics, NGS is considered the optimal strategy for microhaplotype genotyping, and the development of NGS has made microhaplotypes a powerful new type of genetic marker for forensic analyses 2 . Zhu et al 13 , Qu et al 14 , Turchi et al 12 , and Kidd et al 15 have studied microhaplotypes for forensic applications on the Miseq, HiSeq, Ion Personal Genome Machine (PGM), and Ion S5 ™ platforms, respectively. Attempts to develop NGS-based microhaplotype panels and microhaplotype population data have also been reported.…”

Section: Continuedmentioning

confidence: 99%

“…In 2017, 89 microhaplotypes were sequenced with two primer pools in 73 Italian samples 12 , and this panel was later optimized to 87 loci by the same research group 16 . Another research team constructed a 74-plex microhaplotype assay and sequenced 278 samples from three different populations 15 . In the present study, we developed and evaluated a multiplex amplification system containing 124 microhaplotype loci.…”

Section: Continuedmentioning

confidence: 99%

A 124-plex Microhaplotype Panel Based on Next-generation Sequencing Developed for Forensic Applications

Pang

Rao

Chen

et al. 2020

Sci Rep

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Microhaplotypes are an emerging type of forensic genetic marker that are expected to support multiple forensic applications. Here, we developed a 124-plex panel for microhaplotype genotyping based on next-generation sequencing (NGS). The panel yielded intralocus and interlocus balanced sequencing data with a high percentage of effective reads. A full genotype was determined with as little as 0.1 ng of input DNA. Parallel mixture experiments and in-depth comparative analyses were performed with capillary-electrophoresis-based short tandem repeat (STR) and NGS-based microhaplotype genotyping, and demonstrated that microhaplotypes are far superior to STRs for mixture deconvolution. DNA from Han Chinese individuals (n = 256) was sequenced with the 124-plex panel. In total, 514 alleles were observed, and the forensic genetic parameters were calculated. A comparison of the forensic parameters for the 20 microhaplotypes with the top A e values in the 124-plex panel and 20 commonly used forensic STRs showed that these microhaplotypes were as effective as STRs in identifying individuals. A linkage disequilibrium analysis showed that 106 of the 124 microhaplotypes were independently hereditary, and the combined match probability for these 106 microhaplotypes was 5.23 × 10 −66. We conclude that this 124-plex microhaplotype panel is a powerful tool for forensic applications. The microhaplotype is a powerful new type of forensic genetic marker 1,2. It is the combination of two or more closely linked single-nucleotide polymorphisms (SNPs) within DNA segments of 200 base pairs (bp), and offers multiple forensic applications 3-7. Short tandem repeat (STR) genotyping is currently the dominant technology in forensic DNA laboratories. Although it works well with single-sourced DNA samples, great challenges are encountered with DNA mixtures because stutters in the major donor DNA can be indistinguishable from alleles in the minor donor DNA 3,8. Stutters are unavoidable during the replication of repetitive DNA, and they severely interfere with mixture deconvolution. SNPs are not repetitive sequences, but are typically biallelic, which restricts their utility in the analysis of mixtures. Microhaplotypes have the advantages of both STRs and SNPs because they are multiallelic and do not produce stutters during amplification. Therefore, microhaplotypes are perfect genetic markers for mixture deconvolution. Although capillary electrophoresis (CE)-based genetic analyzers are widely used in forensic DNA laboratories, these machines are unsuitable for microhaplotype genotyping 8. Several methods have been used for microhaplotype detection. TaqMan assays have been used to type each SNP that constitutes a microhaplotype 8 , followed by a PHASE software analysis to determine the cis/trans relationships between individual SNP alleles. Single-strand conformational polymorphisms 9 and high-resolution melting curves 4 have also been used for microhaplotype genotyping. These methods are simple and inexpensive, but they can pose problems when multipl...

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“…Another notable benefit of microhaps is that they can be selected not only for high within -population variation, but also for high between -population variation, facilitating prediction of biogeographic ancestry (Oldoni et al, 2017; Zhu et al, 2019; Chen et al, 2019b). It is thus possible to design a comprehensive forensic panel using a combination of microhap and SNP markers that will enable identification, mixture detection and deconvolution (Bennett et al, 2019), ancestry inference, and prediction of externally visible characteristics (Walsh et al, 2013; Ruiz et al, 2013; Crawford et al, 2017) in a single NGS-based assay.…”

Section: Introductionmentioning

confidence: 99%

MicroHapDB: a portable and extensible database of all published microhaplotype marker and frequency data

Standage

Mitchell²

2020

Preprint

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2Microhaplotypes are the subject of significant interest in the forensics community as a promising 3 multi-purpose forensic DNA marker for human identification. Microhaplotype markers are 4 composed of multiple SNPs in close proximity, such that a single NGS read can simultaneously 5 genotype the individual SNPs and phase them in aggregate to determine the associated donor 6 haplotype. Abundant throughout the human genome, numerous recent studies have sought 7 to discover and rank microhaplotype markers according to allelic diversity within and among 8 populations. Microhaplotypes provide an appealing alternative to STR markers for human 9 identification and mixture deconvolution, but can also be optimized for ancestry inference or 10 combined with phenotype SNPs for prediction of externally visible characteristics in a multiplex 11 NGS assay. Designing and evaluating panels of microhaplotypes is complicated by the lack of a 12 convenient database of all published data, as well as the lack of population allele frequency data 13 spanning disparate marker collections. We present MicroHapDB, a comprehensive database of 14 published microhaplotype marker and frequency data, as a tool to advance the development of 15 microhaplotype-based human forensics capabilities. We also present population allele frequencies 16 derived from 26 global population samples for all microhaplotype markers published to date, 17 facilitating the design and interpretation of custom multi-source panels. We submit MicroHapDB 18 as a resource for community members engaged in marker discovery, population studies, assay 19 development, and panel and kit design. 20 Well-studied short tandem repeat (STR) markers have formed the basis of forensic human identification 22 methods since the 1990s. The most common strategy in practice today utilizes several fluorescent dyes 23 to type 20 or more STR markers in a single polymerase chain reaction (PCR) followed by capillary 24 electrophoresis (CE) detection (Butler, 2010). The resulting DNA profiles, combined with STR allele 25 frequency estimates, can then be used to calculate match statistics or evaluate the relative weight of evidence 26 1 Standage & Mitchell MicroHapDB v0.5for competing propositions in a likelihood ratio framework (Butler, 2015; Cowell et al., 2015; Bleka et al., 27 2016a,b). Statistics obtained via STR typing can provide high confidence given the number of independent 28 markers in an assay and the multiallelic nature of each marker. 29 Despite impressive recent improvements in DNA sequencing technologies, next-generation sequencing 30 (NGS) assays of single nucleotide polymorphism (SNP) markers have seen slow adoption for forensic 31 human identification. The ability to genotype sufficient numbers of SNPs to achieve suitable statistical 32 power remains beyond the scope of many forensics laboratories. A relevant factor is the forensics 33 community's strong disinclination, on ethical and privacy grounds, to use DNA markers associated 34 with human disease...

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Microhaplotypes for ancestry prediction

Cited by 22 publications

References 5 publications

Validation of novel forensic DNA markers using multiplex microhaplotype sequencing

Validation of novel forensic DNA markers using multiplex microhaplotype sequencing

A 124-plex Microhaplotype Panel Based on Next-generation Sequencing Developed for Forensic Applications

MicroHapDB: a portable and extensible database of all published microhaplotype marker and frequency data

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