Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes

Wu, Weiwei; Hao, Honglei; Liu, Qiuling; Han, Xian; Wu, Yeda; Cheng, Jianding; Lu, Dalei

doi:10.1007/s00414-014-1032-y

Cited by 12 publications

(7 citation statements)

References 20 publications

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“…Furthermore, ILIR[33] has already been proposed for the incorporation of recombination rate estimates between such closely positioned forensic loci, as a way to reduce the effect of linkage bias in likelihood calculations. Therefore, the optimum combination of four CE kits as described above, aimed at obtaining the most informative genetic data for challenging relationship test scenarios, would only require adjustment of likelihood calculations for a single marker pair amongst the 62 STRs, since the STRtyper kit is not included in this combination and only brings D18S1364 plus the linked D2S1772 as additional loci.It should be mentioned that a study by Wu et al in 2014[34] of linkage data across 12 chromosomes, estimated for the AGCU component STRs using the same HapMap recombination map, obtained identical recombination rate estimates as those reported here.3.3. Population variability and forensic informativeness metrics of newly-adoptedSTRs In all, 35 newly-adopted STRs have full HGDP-CEPH population data published from which allele frequency estimates and forensic informativeness metrics can be obtained in seven worldwide population groups.…”

supporting

confidence: 68%

A genomic audit of newly-adopted autosomal STRs for forensic identification

Phillips

2017

Forensic Science International: Genetics

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In preparation for the growing use of massively parallel sequencing (MPS) technology to genotype forensic STRs, a comprehensive genomic audit of 73 STRs was made in 2016 [Parson et al., Forensic Sci. Int. Genet. 22, 54-63]. The loci examined included miniSTRs that were not in widespread use, but had been incorporated into MPS kits or were under consideration for this purpose. The current study expands the genomic analysis of autosomal STRs that are not commonly used, to include the full set of developed miniSTRs and an additional 24 STRs, most of which have been recently included in several supplementary forensic multiplex kits for capillary electrophoresis. The genomic audit of these 47 newly-adopted STRs examined the linkage status of new loci on the same chromosome as established forensic STRs; analyzed world-wide population variation of the newly-adopted STRs using published data; assessed their forensic informativeness; and compiled the sequence characteristics, repeat structures and flanking regions of each STR. A further 44 autosomal STRs developed for forensic analyses but not incorporated into commercial kits, are also briefly described.

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supporting

confidence: 68%

A genomic audit of newly-adopted autosomal STRs for forensic identification

Phillips

2017

Forensic Science International: Genetics

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“…Recombination fraction can be derived from genetic map or calculated from family data. Genetic maps may present an overestimation or an underestimation of the recombination fraction . In this study, recombination fractions based on the Rutgers Map for the STR pairs D3S2402‐D3S2452, D3S2452‐D3S1766, D3S4554‐D3S2388, and D3S3051‐D3S3053 were obvious underestimates in compare to those from family data.…”

Section: Discussionmentioning

confidence: 50%

“…For close syntenic STR loci, a concern of the forensic community was whether or not physical linkage had an effect on forensic biostatistics. Although a few previous papers have concluded that linkage of STRs would not likely to result in LD [26][27][28], LD between adjacent STRs was still found at clus-terⅣ: D4S2404-D4S2364 and clusterⅥ: D17S975-D17S1294. Compared with those linked STR markers studied previously [26][27][28], we noted that the recombination fractions within the two clusters is very small (Ͻ0.003).…”

Section: Relation Between Linkage Disequilibrium and Recombinationmentioning

confidence: 99%

Potential of 13 linked autosomal short tandem repeat loci in pairwise kinship analysis

Liu

Xue

et al. 2016

Electrophoresis

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In this study, a panel of 13 STR loci locate on chromosome 3, 4, and 17 (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2404, D4S2364, AC001348A, AC001348B, D17S975, and D17S1294) were assessed for pairwise kinship analysis. Map distances between these STR loci ranged from 0.07 cM to 97.03 cM. The population genetic study of Chinese Han population showed that linkage disequilibrium exists in two clusters of closely linked markers (D4S2404-D4S2364 and D17S975-D17S1294), in which the recombination fractions were 0.0026 and 0.0001, respectively. The recombination fractions derived from the Rutgers Map for the closely linked markers (genetic distance < 0.5 cM) were significant underestimates in comparison to those of direct observation of STR transmissions in families. When effect of linkage on pairwise kinship testing was evaluated by comparing likelihood ratio (LR) values taking linkage into account, overall LR values increased. But extremely low LRs were also observed. Finally, the power of the 13 STR loci to discriminate relationship among full-sibs, half-sibs, grandparent-grandchild, uncle-niece, and unrelated pairs was assessed with a category fraction. The results showed that about 72.64% of full-sib pairs and about 82.84% of unrelated pairs could be classified correctly. But the category fractions of second-degree relationships drastically reduced to 7.34-35.48%. If only pairs of grandparent-grandchild, half-sibs, and uncle-niece were distinguished, the category fraction was 0.5512, 0.1147, and 0.4362, respectively. Our study results demonstrated that linked STRs were helpful to differentiate the most frequent relationships in pairwise kinship analysis.

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“…As recombination rates vary along chromosomes, using the physical distance (per bp) may underestimate or overestimate the genetic distance between syntenic loci 21 . Therefore, family studies have been undertaken to estimate the recombination fraction (RF) between syntenic loci 21–24 . However, family studies are expensive and, sometimes, may not be informative enough due to the need of a large number of generations (meiosis) and high percentage of heterozygote genotypes 4,22 .…”

Section: Introductionmentioning

confidence: 99%

“…The data of the 17 non-CODIS loci were merged with the data of 21 STRs generated from the same samples 26 , and were used for testing potential linkage between syntenic loci (linkage disequilibrium, LD). RF values of syntenic pairs were reviewed from 4,12,21,22,24 , which were estimated using family studies and using HapMap data. RFs derived from HapMap data for D2S1338-D2S441, TPOX-D2S1338, FGA-D4S2366 and D5S2800-CSF1PO pairs, were calculated based on cumulative genetic map distance provided by Phillips 12 and using the Excel tool developed by Phillips et al .…”

Section: Introductionmentioning

confidence: 99%

An evaluation of the SureID 23comp Human Identification Kit for kinship testing

Alsafiah

Aljanabi

Hadi

et al. 2019

Sci Rep

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Short tandem repeat (STR) profiling has been routinely used in kinship testing since the introduction of commercial kits in the mid-1990s. While 15 to 23 STR loci normally give definitive results in simple kinship testing, additional loci are sometimes required to resolve complex cases. The SureID 23comp Human Identification Kit, recently released by Health Gene Technologies (China), multiplexes amelogenin and 22 autosomal STRs, 17 of which are non-CODIS STRs. This enables the profiling of 38–40 loci when used in conjunction with widely used commercial kits. In this study, the kit was evaluated for kinship applications as a supplementary STR kit following the minimum criteria for validation recommended by the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) using 500 samples. Performance was comparable with other commercial kits demonstrating: repeatability and reproducibility; precision (maximum s.d. 0.1048 nt); accuracy, all alleles were within ±0.41 nt compared to the actual sizes; heterozygous peak balances at all loci >68%; stutter ratios ranged from 3.8% to 16.15%; full profiles were generated with 125 pg DNA (95.12% of alleles at 62 pg),; and we found 100% concordance over 5 common STRs with the GlobalFiler kit.

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Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes

Cited by 12 publications

References 20 publications

A genomic audit of newly-adopted autosomal STRs for forensic identification

A genomic audit of newly-adopted autosomal STRs for forensic identification

Potential of 13 linked autosomal short tandem repeat loci in pairwise kinship analysis

An evaluation of the SureID 23comp Human Identification Kit for kinship testing

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