Mutation analysis of 28 autosomal short tandem repeats in the Chinese Han population

Huang, Yujie; Liu, Cong; Xiao, Changfu; Chen, Xiaoying; Han, Xueli; Yi, Shaohua; Huang, Daixin

doi:10.1007/s11033-021-06522-7

Cited by 6 publications

(3 citation statements)

References 19 publications

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“…Mutations detected in both cases were from paternal source, what was supported by the statement that the mutations occur more often in sperm cells compared to the female egg cells (Qian et al, 2015). Other studies have also found that paternal mutations occur more frequently than maternal not only at autosomal STR loci (Huang et al, 2021) but X-linked STR loci as well (Pinto et al, 2020).…”

Section: Discussionsupporting

confidence: 65%

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2022

JJBS

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Instructions to AuthorsScopes Study areas include cell biology, genomics, microbiology, immunology, molecular biology, biochemistry, embryology, immunogenetics, cell and tissue culture, molecular ecology, genetic engineering and biological engineering, bioremediation and biodegradation, bioinformatics, biotechnology regulations, gene therapy, organismal biology, microbial and environmental biotechnology, marine sciences. The JJBS welcomes the submission of manuscript that meets the general criteria of significance and academic excellence. All articles published in JJBS are peerreviewed. Papers will be published approximately one to two months after acceptance.

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Section: Discussionsupporting

confidence: 65%

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2022

JJBS

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“…In human forensic sciences, INDELs have been noted as markers for individual identification testing [ 26 , 27 ] because they are diallelic, small in size, and widely distributed throughout the genome. Furthermore, INDELs have the advantage of lower mutation rates than SNPs and short tandem repeats (STRs) [ 28 ]. In the present study, we propose 97,443 INDELs (chromosome: autosomes, allele number: diallelic, size: −2 to −4 and +2 to +4, allele frequency: 0.25 to 0.75, excluding INDELs with all heterozygous genotypes) as marker candidates to construct a panel of horse parentage testing.…”

Section: Discussionmentioning

confidence: 99%

Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses

Tozaki

Ohnuma

Kikuchi

et al. 2023

Genes

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Thoroughbreds are some of the most famous racehorses worldwide and are currently animals of high economic value. To understand genomic variability in Thoroughbreds, we identified genome-wide insertions and deletions (INDELs) and obtained their allele frequencies in this study. INDELs were obtained from whole-genome sequencing data of 101 Thoroughbred racehorses by mapping sequence reads to the horse reference genome. By integrating individual data, 1,453,349 and 113,047 INDELs were identified in the autosomal (1–31) and X chromosomes, respectively, while 18 INDELs were identified on the mitochondrial genome, totaling 1,566,414 INDELs. Of those, 779,457 loci (49.8%) were novel INDELs, while 786,957 loci (50.2%) were already registered in Ensembl. The sizes of diallelic INDELs ranged from −286 to +476, and the majority, 717,736 (52.14%) and 220,672 (16.03%), were 1-bp and 2-bp variants, respectively. Numerous INDELs were found to have lower frequencies of alternative (Alt) alleles. Many rare variants with low Alt allele frequencies (<0.5%) were also detected. In addition, 5955 loci were genotyped as having a minor allele frequency of 0.5 and being heterogeneous genotypes in all the horses. While short-read sequencing and its mapping to reference genome is a simple way of detecting variants, fake variants may be detected. Therefore, our data help to identify true variants in Thoroughbred horses. The INDEL database we constructed will provide useful information for genetic studies and industrial applications in Thoroughbred horses, including a gene-editing test for gene-doping control and a parentage test using INDELs for horse registration and identification.

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“…This property enables one to identify a specific individual based on genotyping the STR variations. This application is the basis of widely used forensic applications, , population and disease studies, − as well as cell line profiling. − Their presence is also related to secondary DNA motifs like hairpins or G quadruplex complexes and serious pathologies such as cancer, , among others. − …”

Section: Introductionmentioning

confidence: 99%

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

Hernández Bustos,

Martiny,

Bom Pedersen

et al. 2023

Anal. Chem.

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We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.

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Mutation analysis of 28 autosomal short tandem repeats in the Chinese Han population

Cited by 6 publications

References 19 publications

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Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay

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