Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

Abstract

Massively parallel sequencing (MPS) has rapidly become a promising method for forensic DNA typing, due to its ability to detect a large number of markers and samples simultaneously in a single reaction, and sequence information can be obtained directly. In the present study, two kinds of forensic genetic markers, short tandem repeat (STR) and identity-informative single nucleotide polymorphism (iiSNP) were analyzed simultaneously using ForenSeq DNA Signature Prep Kit, a commercially available kit on MPS platform. A total of 152 DNA markers, including 27 autosomal STR (A-STR) loci, 24 Y chromosomal STR (Y-STR) loci, 7 X chromosomal STR (X-STR) loci and 94 iiSNP loci were genotyped for 107 Tibetan individuals (53 males and 54 females). Compared with length-based STR typing methods, 112 more A-STR alleles, 41 more Y-STR alleles, and 24 more X-STR alleles were observed at 17 A-STRs, 9 Y-STRs, and 5 X-STRs using sequence-based approaches. Thirty-nine novel sequence variations were observed at 20 STR loci. When the flanking regions were also analyzed in addition to target SNPs at the 94 iiSNPs, 38 more alleles were identified. Our study provided an adequate genotype and frequencies data of the two types of genetic markers for forensic practice. Moreover, we also proved that this panel is highly polymorphic and informative in Tibetan population, and should be efficient in forensic kinship testing and personal identification cases. Several genetic markers have been introduced to forensic genetics to clarify the problems of kinship analysis and personal identification. Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are commonly used genetic markers in present forensic cases 1,2. STRs, usually 2-6 bp in length, are commonly typed with the amplified fragment length polymorphism (Amp-FLP) strategy combining fluorescently labelled multiplex PCR and capillary electrophoresis (CE) 3. Allele calling can thus be inferred from fragment length by comparison with a locus specific allelic ladder that has been previously sequenced, where the number of repeat units is distinct 2. Thus, each allele is regarded as a lengthbased (LB) allele using this approach. With the advancement of sequencing technologies over the last decade, the existence of sequence structure variations in alleles with the same length has been uncovered 4. SNPs, which could be amplified with smaller amplicons, are bi-allelic genetic markers with lower mutation rates compared with STRs 5. Several autosomal SNP marker sets and detection methods, such as single-base extension, chip-based microarrays, and allele-specific hybridization arrays, have been developed to compensate for the relatively weaker discrimination power of single loci caused by the bi-allelic nature of the human genome 5-7. However, these methods are not widely used in forensic practice due to the requirement of higher DNA inputs or the limited ability to detect a vast number of SNP loci in a single reaction 8. Different from detection methods mentioned above, massively paralle...

Characterization of 58 STRs and 94 SNPs with the ForenSeq™ DNA Signature Prep Kit in Mexican-Mestizos from the Monterrey City (Northeast, Mexico)

“…The number of different alleles found here (528 different STR alleles) was higher than those reported in Spanish French [4], Asian [5], and Peruvian [6] populations. Also, our RSB results improve importantly the combined PD and CE compared with those previously obtained in Monterrey City but based on 23 aSTRs genotyped by CE [19].…”

“…These results may be caused by sampling errors, especially when it comes from a cosmopolitan population such as Monterrey City, the second-most-important metropolis in Mexico. Although a larger population sample size could exhibit more allele diversity, producing more accurate estimates, we were able to observe as far as 367 different aSTR alleles, which is similar or superior to previous studies with the DPS-A of the ForenSeq™ DNA Signature Prep [3][4][5].…”

“…MPS is getting widespread acceptance in forensic genetics because of its throughput generating information on a much higher number of markers and sequencing of short tandem repeats (STRs), which allows allele discrimination with the same length but different sequences that enhance its potential in human identi cation (HID). Moreover, MPS platforms allow detecting different markers simultaneously, such as STRs, SNPs, and insertion-deletions (InDels) [1][2][3][4][5][6][7][8]. For these reasons, several commercial PCR-MPS assays for human identi cation have been introduced and evaluated by forensic genetic labs [2,3,[7][8][9][10][11].…”

RETRACTED: Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population

“…Among the 653 unique sequence‐based alleles (including the flanking region) observed in this study, 35 identified in 25 loci (12 A‐STRs loci, 11 Y‐STR loci, and 2 X‐STRs loci, respectively) were not recorded in the STR Sequencing Project (Gettings et al, 2017) and have never been reported in any of the previous studies (Barrio et al, 2019; Churchill et al, 2017; Delest et al, 2020; Devesse et al, 2018, 2020; Gettings et al, 2015, 2016; Hussing et al, 2019; Jäger et al, 2017; Khubrani et al, 2019; Kim et al, 2016, 2018; Novroski et al, 2016; Peng et al, 2020; Phillips, Devesse, et al, 2018; Phillips, Gettings, et al, 2018; Wang et al, 2020; Wendt et al, 2017). Sanger sequencing was performed to verify these novel sequence‐based alleles (data not provided) and all 35 are listed in Table 2.…”

Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing

“…X-STRs and Y-STRs were not considered for the PI calculation since little effective information could be obtained for cases presented in this study. As there is no significant LD in the Chinese population for these iiSNPs and A-STRs after Bonferroni correction [22,32], the PI values of iiSNPs and A-STRs were multiplied to calculate the CPI values. When combining the SNP and A-STR marker, 82.35% (14/17), 88.24% (15/17), 94.12% (16/17) and 94.12% (16/17) of real family cases could be accurately determined with an LR threshold for inclusion set as 10,000, 1000, 100 and 10, respectively (Table 3).…”