Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems

Li, Jinliang; Yang, Qinrui; Shao, Chengchen; Liu, Baonian; Zhou, Yuxiang; Xu, Hongmei; Zhou, Yueqin; Tang, Qiqun; Xie, Jianhui

doi:10.1016/j.legalmed.2017.10.007

Cited by 13 publications

(5 citation statements)

References 43 publications

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“…The genotyping concordance of Huaxia™ Platinum Kit with other commercially available kits yielded 100% concordance except at the loci D5S818 and Penta E (Supplemental Table 1). An allele dropout at D5S818 with PowerPlex® 21 has been previously reported [26,27]. The discordance at Penta E with the PowerPlex® 21 kit was due to an allele 27 being out of its marker range.…”

Section: Population and Concordance Studiesmentioning

confidence: 87%

Developmental validation of the Huaxia™ Platinum PCR amplification kit: A 6-dye multiplex direct amplification assay designed for Chinese reference samples

Zhong

Gopinath

Norona

et al. 2019

Forensic Science International: Genetics

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Section: Population and Concordance Studiesmentioning

confidence: 87%

Developmental validation of the Huaxia™ Platinum PCR amplification kit: A 6-dye multiplex direct amplification assay designed for Chinese reference samples

Zhong

Gopinath

Norona

et al. 2019

Forensic Science International: Genetics

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“…All samples were collected from the same districts in Iran, and the results were replicated in both groups. Rare primer binding site mutations are known to provoke null alleles in STRs, and lead to false homozygous genotypes [28][29][30] . In a review by Dakin and Avise, it was reported that whereas null alleles in frequencies typically reported in the literature introduce rather inconsequential biases on average exclusion probabilities, they can introduce substantial errors into empirical assessments of specific mating events by leading to high frequencies of false parentage exclusions 31 .…”

Section: Discussionmentioning

confidence: 99%

A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder

Khamse

Alizadeh

Bernhart

et al. 2022

Sci Rep

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The human SBF1 (SET binding factor 1) gene, alternatively known as MTMR5, is predominantly expressed in the brain, and its epigenetic dysregulation is linked to late-onset neurocognitive disorders (NCDs), such as Alzheimer’s disease. This gene contains a (GCC)-repeat at the interval between + 1 and + 60 of the transcription start site (SBF1-202 ENST00000380817.8). We sequenced the SBF1 (GCC)-repeat in a sample of 542 Iranian individuals, consisting of late-onset NCDs (N = 260) and controls (N = 282). While multiple alleles were detected at this locus, the 8 and 9 repeats were predominantly abundant, forming > 95% of the allele pool across the two groups. Among a number of anomalies, the allele distribution was significantly different in the NCD group versus controls (Fisher’s exact p = 0.006), primarily as a result of enrichment of the 8-repeat in the former. The genotype distribution departed from the Hardy–Weinberg principle in both groups (p < 0.001), and was significantly different between the two groups (Fisher’s exact p = 0.001). We detected significantly low frequency of the 8/9 genotype in both groups, higher frequency of this genotype in the NCD group, and reverse order of 8/8 versus 9/9 genotypes in the NCD group versus controls. Biased heterozygous/heterozygous ratios were also detected for the 6/8 versus 6/9 genotypes (in favor of 6/8) across the human samples studied (Fisher’s exact p = 0.0001). Bioinformatics studies revealed that the number of (GCC)-repeats may change the RNA secondary structure and interaction sites at least across human exon 1. This STR was specifically expanded beyond 2-repeats in primates. In conclusion, we report indication of a novel biological phenomenon, in which there is selection against certain heterozygous genotypes at a STR locus in human. We also report different allele and genotype distribution at this STR locus in late-onset NCD versus controls. In view of the location of this STR in the 5′ untranslated region, RNA/RNA or RNA/DNA heterodimer formation of the involved genotypes and alternative RNA processing and/or translation should be considered.

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“…For STRs, primer binding site mutations are known to provoke null alleles, also known as silent alleles (Yao et al, 2018). A detailed explanation of how null alleles can be identified and circumvented is given by Li et al (2014).…”

Section: Discussionmentioning

confidence: 99%

The transitivity of the Hardy–Weinberg law

Graffelman

Weir

2022

Forensic Science International: Genetics

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Null alleles and sequence variations at primer binding sites of STR loci within multiplex typing systems

Cited by 13 publications

References 43 publications

Developmental validation of the Huaxia™ Platinum PCR amplification kit: A 6-dye multiplex direct amplification assay designed for Chinese reference samples

Developmental validation of the Huaxia™ Platinum PCR amplification kit: A 6-dye multiplex direct amplification assay designed for Chinese reference samples

A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder

The transitivity of the Hardy–Weinberg law

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