Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches

Qian, Xiaoqin; Hou, Jiayi; Wang, Zheng; Ye, Yi; Lang, Min; Gao, Tianxi; Liu, Jing; Hou, Yiping

doi:10.1038/s41598-017-11955-x

Cited by 31 publications

(10 citation statements)

References 32 publications

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“…However, some countries, for example, China (Ge et al, 2013(Ge et al, , 2014 started to accumulate also Y-STR haplotypes in their national DNA databases. In severe crime cases Y chromosome analysis can be seen as a "last resort" technique to collect intelligence information on an unknown perpetrator and to narrow down the number of suspects (Qian et al, 2017;Yao et al, 2016). In Europe a Y-STR profile was used in the elimination process of a mass screening already in 2000 (Dettlaff-Kakol & Pawlowski, 2002) when a serial rapist and murderer called the "Vampire from Świnouj scie" was hunted down in Northern Poland.…”

Section: Investigative Leads Provided By Y-chromosome Testingmentioning

confidence: 99%

Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA

Roewer

2019

WIREs Forensic Science

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The analysis of short tandem repeat (STR) markers located on the Y chromosome is an established method in forensic casework analysis. Usually this method is applied in cases of male‐on‐female sexual assault, in which the victim's DNA is in great excess and masked the male contribution. Y‐STR analysis is able to detect the presence of minuscule amounts of male DNA of one or multiple donors and resulting genetic profiles can be compared to known reference samples. The expert has to determine whether the Y‐STR result of a trace is suitable for a biostatistical calculation in case of a match. The Discrete Laplace method which is implemented in the Y chromosome haplotype reference database (YHRD) can be used to estimate haplotype frequencies with a better approximation than other methods namely the counting method. Moreover, Y‐SNPs in combination with Y‐STRs can infer the biogeographical origin of an unknown male person with comparably high precision due to the availability of a robust phylogenetic tree and large reference data collections. Y‐based ancestry prediction and familial searching can, therefore, provide important investigative leads in crime cases without suspect. This article is categorized under: Forensic Biology > Haploid Markers Forensic Biology > Ancestry Determination using DNA Methods Forensic Biology > DNA Databases and Biometrics Forensic Biology > Forensic DNA Technologies

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Section: Investigative Leads Provided By Y-chromosome Testingmentioning

confidence: 99%

Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA

Roewer

2019

WIREs Forensic Science

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“…Based on our previously published panels [11, 18, 19] and unpublished experimental data, 164 Y‐SNPs were selected that showed diverse genetic polymorphisms in several Chinese groups. Haplogroups CT, C, DE, D, F, G, H, I, J, K, LT, L, N, O, P, Q, and R and their subhaplogroups were covered in the 164 Y‐SNPs genotyping system.…”

Section: Methodsmentioning

confidence: 99%

“…Due to male‐specific characteristics, genetic markers on the nonrecombining Y chromosome region have been a powerful tool in forensic research and practice including genealogy research, population genetics, individual identification, and paternity testing [7–10]. With an extremely low mutation rate (3 × 10 −8 mutations/generation), Y‐chromosome single nucleotide polymorphisms (Y‐SNPs) can provide a stable lineage genetic signature, by which people can be divided into different haplogroups and subhaplogroups [8, 11]. Recently, more Y‐SNPs have been discovered and phylogenetically mapped, but the population data are still scarce in some groups such as the Yi.…”

Section: Introductionmentioning

confidence: 99%

Genetic reconstruction and phylogenetic analysis by 193 Y‐SNPs and 27 Y‐STRs in a Chinese Yi ethnic group

Wang

Song

et al. 2021

Electrophoresis

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Yi is the seventh‐largest ethnic group in China and features mountainous regional characteristics. The Liangshan Yi Autonomous Prefecture is the largest Yi agglomeration with isolated geographical conditions, profoundly impeding genetic communication. Here, we investigated 427 unrelated males of Liangshan from 193 Y‐chromosome single nucleotide polymorphisms (Y‐SNPs) and 27 Y‐chromosome short tandem repeats (Y‐STRs) to reveal the genetic structure and paternal phylogeny of the group. The haplogroup diversity reached 0.9169 with 46 different subhaplogroups by 193 Y‐SNPs, and the haplotype diversity reached 0.9999 by 27 Y‐STR loci. Multidimensional scaling (MDS), N‐J tree, and Network were constructed to decipher and visualize the genetic relations between Yi and worldwide groups. Our results revealed: (1) the Network by Y‐STRs and Y‐SNPs showed the haplogroup D1a1a‐M15 in the Liangshan Yi population was a ramification of Tibetan groups’ expansion from west to east on the plateau; (2) the haplogroup distribution and the mismatch mutation analysis indicated the haplogroup O2a2b1a1a1a4a2‐Z25929 of Liangshan Yi derived from manifold Southeast Asian immigrants; (3) a high‐resolution Y‐SNPs panel is vital to depict accurate paternal derivations and build an integrated and refining genetic structure of ethnic groups.

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“…In recent years, several different methods and technologies have been widely utilized for SNP genotyping, like SNaPshot, massively parallel sequencing (MPS) (or nextgeneration sequencing; NGS), and DNA mass spectrometry (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; MALDI-TOF MS) [9][10][11][12][13][14][15]. SNaPshot technology is a very sensitive detection method, but its fairly limited multiplexing capability greatly limits the resolution of the achievable Y haplogroup.…”

Section: Introductionmentioning

confidence: 99%

Development and validation of a custom panel including 183 Y‐SNPs for Chinese Y‐chromosomal haplogroups dissection using a MALDI‐TOF MS system

Zhang

Luo

et al. 2020

Electrophoresis

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Y‐chromosome SNP haplogroups exhibit geographic structuring in many populations around the world. Therefore, Y‐chromosome haplogroups have been widely used to infer paternal biogeographical ancestry and high‐resolution paternal lineage classification. In the present study, we designed a customized panel containing 183 Y‐SNPs based on previous studies and evaluated the genotyping performance and repeatability, concordance, sensitivity, and ability of analysing case‐type samples using a MALDI‐TOF MS platform. The average call rate for duplicate typing of any one SNP in the panel was 97.0%. In the concordance and accuracy study, the results of haplogroup designation obtained from MALDI‐TOF MS platform were fully consistent with those obtained from the next‐generation sequencing (NGS) platform. The optimal amount of template DNA in the PCR seemed to be 10 ng. However, if less DNA (≥156.25 pg) was available, it was still possible to obtain meaningful haplogroup information. For the application part, this panel could be applied for the detection of blood, semen, and buccal swabs samples. Particularly, blood stain on FTA card samples could be dissected by direct PCR amplification on the MALDI‐TOF MS platform. Besides, 371 unrelated male individuals from four Chinese ethnic groups (Han, Hui, Mongolian, and Kazak) were detected using this panel. Total 78 terminal haplogroups were found and the haplogroup diversity was 0.933576. The results demonstrate that this panel could be an accurate, fast, and cost‐effective method for database construction where the amount of sample material is less of a concern and when the cost of the assay is taken into consideration.

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Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches

Cited by 31 publications

References 32 publications

Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA

Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA

Genetic reconstruction and phylogenetic analysis by 193 Y‐SNPs and 27 Y‐STRs in a Chinese Yi ethnic group

Development and validation of a custom panel including 183 Y‐SNPs for Chinese Y‐chromosomal haplogroups dissection using a MALDI‐TOF MS system

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