Triallelic patterns in STR loci used for paternity analysis: Evidence for a duplication in chromosome 2 containing the TPOX STR locus

Lukka, Matti; Tasa, Gunnar; Ellonen, Pekka; Moilanen, Kirsi; Vassiljev, Vitali; Ulmanen, Ismo

doi:10.1016/j.forsciint.2005.11.006

Cited by 22 publications

(13 citation statements)

References 23 publications

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“…There are two types of triallelic patterns: type 1 where after polymerase chain reaction (PCR) amplification, the first two peaks have a different intensity than the third visualized peak and this type refers to the condition when a mutation occurs in early somatic cells and type 2 where after PCR amplification, three similar peaks are seen and this is associated with a constitutional chromosomal rearrangement (Clayton et al, 2004). The type 2 triallelic pattern can either be associated with clinical symptoms or have a minimal effect on normal development, depending on whether the cause behind this pattern is a chromosomal duplication or a partial maternal isodisomy for chromosome 2p, respectively (Bakker et al, 2001;Lukka et al, 2006). Moreover, and as per Lane (2008), TPOX triallelic genotype is a condition affecting females to a higher extent than males, and fathers with this condition transmitted this genotype to their female descendants only, proposing that the additional allele is located on the X chromosome.…”

Section: Introductionmentioning

confidence: 99%

TPOX Triallelic Genotype: An Interesting Pattern to Be Noted in Bone Marrow Transplantation Monitoring

HoteitRouba

Abdul²,

AntarAhmad³

et al. 2015

Genetic Testing and Molecular Biomarkers

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Section: Introductionmentioning

confidence: 99%

TPOX Triallelic Genotype: An Interesting Pattern to Be Noted in Bone Marrow Transplantation Monitoring

HoteitRouba

Abdul²,

AntarAhmad³

et al. 2015

Genetic Testing and Molecular Biomarkers

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“…2004; Nishimura et al. 2005; Lukka et al. 2006), mutations in primer‐binding sequences (Clayton et al.…”

Section: Discussionmentioning

confidence: 99%

“…2004) or chromosomal gains (Ibanez et al. 2004; Lukka et al. 2006) are known to yield more than two peaks.…”

Section: Introductionmentioning

confidence: 99%

A chromosomal duplication that includes the canine microsatellite INRA21 in Labrador Retrievers

Onogi

Nurimoto

Sato³

et al. 2008

Animal Genetics

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INRA21 is one of the canine microsatellites recommended for parentage verification by the International Society for Animal Genetics. In Labrador Retrievers, abnormal peak patterns such as three-peak patterns during capillary electrophoresis were frequently observed at INRA21. Pedigree analysis indicated that the abnormal peak patterns were due to inheritable causes, and semiquantitative multiplex (SQM) PCR analysis showed that the abnormal peak patterns were caused by chromosomal duplication. Walking SQM-PCR analysis revealed that the size of the duplicated segment was approximately 1.58 Mb. Genotypes of microsatellites within the duplicated segment indicated that the duplication was an identical-by-descent mutation. This duplication is probably carried by more than half of the dogs in the Japanese population of Labrador Retrievers. The abnormal peak patterns at INRA21 were also observed in German Shorthaired Pointers and Flat-Coated Retrievers. Genotyping analysis of the microsatellites within the duplicated segment in Labrador Retrievers suggested that the abnormal peak patterns observed in the two breeds were due to the duplication inherited from the same ancestor as the duplication of Labrador Retrievers. This study urges attention to the use of INRA21 and shows an example of copy number polymorphisms that are characteristic to dog breeds or lineages.

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“…Presently two patterns are known: type 1 (three imbalanced alleles) and type 2 (one imbalanced allele peak). Tri-allelic genotypes have also been identified to be of significant importance in paternity as well as forensic cases [53,55,56]. Tri-allelic genotypes, while a rare variant, do occur frequently, with 388 variants reported for autosomal STRs as of 09/11/2015 in the NIST STR database (http://www.cstl.nist.gov/biotech/strbase/tri_tab.htm) with TPOX (19 variants) and FGA (40 variants) displaying the most observations and several hundred profiles from previous studies [15,53,57,58].…”

Section: Tri-allelic Patternsmentioning

confidence: 99%

“…All individuals displaying tri-allelic patterns in this study presented this allele. Frequencies of tri-alleles, for the locus TPOX, below 0.006 were observed in non-African regions [53][54][55]57,59]. Greater frequencies (0.004-0.045) have been observed in African populations [15,[60][61][62], and the Dominican republic [58].…”

Section: Tri-allelic Patternsmentioning

confidence: 99%

GlobalFiler ® Express DNA amplification kit in South Africa: Extracting the past from the present

Ristow

Cloete

D’Amato

2016

Forensic Science International: Genetics

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In this study, the GlobalFiler(®) Express amplification kit was evaluated for forensic use in 541 South African individuals belonging to the Afrikaaner, amaXhosa,(1) amaZulu,(1) Asian Indian and Coloured population groups. Allelic frequencies, genetic diversity parameters and forensic informative metrics were calculated for each population. A total of 301 alleles were observed ranging between 5 and 44.2 repeat units, 43 were rarely observed partial repeats and seven were novel. The combined match probability (CMP) ranged from 2.21×10(-26) (Coloured) to 5.21×10(-25) (AmaZulu), and the combined power of exclusion (CPE) 0.9999999978 (Afrikaaner) to 0.99999999979 (AmaZulu) respectively. No significant departures from Hardy-Weinberg equilibrium (HWE) were observed after Bonferroni correction. Strong evidence of genetic structure was detected using the coancestry coefficient θ, Analysis of Molecular Variance (AMOVA) and an unsupervised Bayesian clustering method (STRUCTURE). The efficiency of assignment of individuals to population groups was evaluated by applying likelihood ratios with WHICHRUN, and the individual ancestral membership probabilities inferred by STRUCTURE. Likelihood ratios performed the best in the assignment of individuals to population groups. Signs of positive selection were detected for TH01 and D13S317 and purifying/balancing selection for locus SE33. These three loci also displayed the largest informativeness for assignment (In) values. The results of this study supports the use of the GlobalFiler(®) STR profiling kit for forensic applications in South Africa with the additional capability to predict ethnicity or continental origin of a random sample.

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Triallelic patterns in STR loci used for paternity analysis: Evidence for a duplication in chromosome 2 containing the TPOX STR locus

Cited by 22 publications

References 23 publications

TPOX Triallelic Genotype: An Interesting Pattern to Be Noted in Bone Marrow Transplantation Monitoring

TPOX Triallelic Genotype: An Interesting Pattern to Be Noted in Bone Marrow Transplantation Monitoring

A chromosomal duplication that includes the canine microsatellite INRA21 in Labrador Retrievers

GlobalFiler ® Express DNA amplification kit in South Africa: Extracting the past from the present

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