An 18 Multi‐InDels panel for analysis of highly degraded forensic biological samples

Li, Jienan; Lin, Lin; Jiang, Bowei; Wang, Chudong; Zeye, Moutanou Modeste Judes; Wen, Dan; He, Wei; Qu, Weifeng; Liu, Ying; Zha, Lagabaiyila

doi:10.1002/elps.202000245

Cited by 10 publications

(8 citation statements)

References 29 publications

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“…With DNA heated for 10 h, three STR loci showed allele‐dropout with the Investigator 26plex QS Kit, while the other two kits had an entire profile with all target markers. Such results were comparable to Li's research [15].…”

Section: Resultssupporting

confidence: 92%

“…Multi-InDel markers have such many advantages, such as high polymorphism, low mutation rate as SNP, small amplicons, and simply detected with CE instruments. Besides, many studies have concentrated on the Multi-InDel markers and several multiplex systems have been established, the probability of exclusion was approximately 0.99, which was not sufficient for parentage test [15]. It is necessary to explore new Multi-InDel markers to enrich the application in parentage test in the future.…”

Section: Introductionmentioning

confidence: 99%

“…However, the PD value of single InDel is much lower than STRs when the number of loci is similar [9], otherwise, more loci are needed [10]. To improve InDel's DP value, some studies suggested that Multi‐InDel markers that have more than two InDel loci within one marker have a powerful PD value in forensic medicine and genetics [11–15]. The genotyping of Multi‐InDel markers could be obtained by a pair of PCR primers and CE, which is compatible with the techniques for STR typing.…”

Section: Introductionmentioning

confidence: 99%

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A new set of 20 Multi‐InDel markers for forensic application

Liu

Zhang

et al. 2022

Electrophoresis

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Insertion/deletion markers (InDels) become an important marker for forensic medicine because of their compatible typing techniques with STRs and lower mutation rates. Recent years, a new kind of DNA marker named Multi-InDel was reported as characterized by two or more tightly linked InDel loci within a short length of physical position, usually 200-300 nucleotides. Many pieces of research showed that Multi-InDels had excellent application values in ancestry inference and forensic medicine. Since the identical number of insertion/deletion nucleotides of the InDel markers that composing the Multi-InDel marker, the genotypes of most reported Multi-InDels could not be directly typed by capillary electrophoresis (CE) due to the lack of length discrepancy among the composing InDel sequence. In this study, we applied a typing system of 20 Multi-InDels including 41 InDels, whose genotypes could be deduced by CE and assessed their potential applications in forensic medicine. A total of 200 unrelated Chinese Han individuals and five mother-child-father trios with proven paternity with one STR locus transmission incompatibilities from Shanxi province were genotyped by the multiplex system. The results showed that a total of 70 specific alleles were observed, more than three alleles were observed in 19 loci and seven alleles were observed in one locus. The combined probability of exclusion and the combined power of discrimination were 0.992 and 0.99999999993, respectively. This study demonstrates their potential usefulness for individual identification and paternity tests. The development of Multi-InDels provided another genetic tool inherent in higher polymorphic and lower mutation rates.

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Section: Resultssupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A new set of 20 Multi‐InDel markers for forensic application

Liu

Zhang

et al. 2022

Electrophoresis

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“…MM-InDel loci with three alleles accounted for 85.59% of the obtained candidates. Additionally, previous studies suggested that MM-InDels containing two InDels have three instead of four alleles ( Huang et al, 2014 ; Li et al, 2021 ), which is in line with our observation. Since it is difficult for multi-allelic InDels to repeatedly mutate into an identical allele and multi-InDels with two InDel loci presented a tri-allelic pattern in the population, a secondary mutation event could be inferred at these loci.…”

Section: Discussionsupporting

confidence: 93%

Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome

Sun

Yang

et al. 2022

Front. Genet.

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Multiple mutational events of insertion/deletion occurring at or around InDel sites could form multi-allelic InDels and multi-InDels (abbreviated as MM-InDels), while InDels with random DNA sequences could imply a unique mutation event at these loci. In this study, preliminary investigation of MM-InDels with random sequences was conducted using high-throughput phased data from the 1000 Genomes Project. A total of 3,599 multi-allelic InDels and 6,375 multi-InDels were filtered with multiple alleles. A vast majority of the obtained MM-InDels (85.59%) presented 3 alleles, which implies that only one secondary insertion or deletion mutation event occurred at these loci. The more frequent presence of two adjacent InDel loci was observed within 20 bp. MM-InDels with random sequences presented an uneven distribution across the genome and showed a correlation with InDels, SNPs, recombination rate, and GC content. The average allelic frequencies and prevalence of multi-allelic InDels and multi-InDels presented similar distribution patterns in different populations. Altogether, MM-InDels with random sequences can provide useful information for population resolution.

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“…Li et al evaluated the effect of the temperature at the 18 multi-InDels panels by keeping DNA isolates in a water bath at 100˚C for 0, 20, 40, 60, and 80 mins. Although all loci were observed in all time intervals, peak imbalances have begun to appear in the alleles after the 40th min [24]. The denaturation of DNA begins at 95˚C…”

Section: Degradation Studiesmentioning

confidence: 97%

A Novel Panel of 36 Insertion/Deletion (InDel) Markers for Human Identification

Filoğlu

Duvenci

Tas

et al. 2022

Preprint

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Background: In recent years, the insertion/deletion (InDel) polymorphism has become a preferred genetic marker in forensic genetics due to its low mutation rates and small amplicon sizes. In this study, a 36-InDelplex identification panel, consisting of autosomal 34 InDel loci, 1 Y InDel locus, and amelogenin, was developed and gene frequencies in the Turkish population were determined. Methods and Results: The loci of the InDel panel with global minimum allele frequencies (MAF) ≥ 0.4 were selected from the 1000 Genomes Project Phase 3 data. The amplicon sizes of the loci were designed to be smaller than 250 bp. In the validation study of the created panel, analysis threshold, dynamic range, sensitivity, stochastic threshold, inhibitor tolerance, and reproducibility parameters were studied in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) guideline. The sensitivity studies indicated that complete and reliable InDel profiles could be obtained with 0.25 ng of DNA. The 36-InDelplex panel was evaluated using the 250 samples from individuals of Turkey. The mean observed heterozygosity ratio (Ho) of all loci was 0.48. Combined discrimination power (CPD) is 0.999999999999988 and combined exclusion probability (CPE) is 0.9987. The population comparison also made using Turkish and each of the five major populations 1000 Genomes Phase 3 populations’ data for each of the five major populations (i.e., African, European, East Asian, South Asian, and American). Conclusions: The results showed that the 36-InDelplex panel is a reliable, sensitive and accurate system, which is suitable for human identification and population genetics purposes.

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An 18 Multi‐InDels panel for analysis of highly degraded forensic biological samples

Cited by 10 publications

References 29 publications

A new set of 20 Multi‐InDel markers for forensic application

A new set of 20 Multi‐InDel markers for forensic application

Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome

A Novel Panel of 36 Insertion/Deletion (InDel) Markers for Human Identification

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