scholarly journals Systematic analysis of short tandem repeats in 38,095 exomes provides an additional diagnostic yield

2020 ◽  
Author(s):  
Bart P.G.H. van der Sanden ◽  
Jordi Corominas ◽  
Michelle de Groot ◽  
Maartje Pennings ◽  
Rowdy P.P. Meijer ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Movement Disorder ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Diagnostic Yield ◽  
Genetic Disorders ◽  
Systematic Analysis ◽  
Str Analysis ◽  
Manual Curation ◽  
Short Tandem

AbstractPurposeThe expansion of specific short tandem repeats (STRs) can lead to approximately 30 different human genetic disorders. Despite extensive application of exome sequencing (ES) in routine diagnostic genetic testing, STRs are not routinely identified from these data.MethodsWe assessed diagnostic utility by applying ExpansionHunter to 2,867 exomes from movement disorder patients and 35,228 other clinical exomes.ResultsWe identified 36 movement disorder patients with a possible aberrant STR length. Validation by PCR and/or repeat-primed PCR technologies confirmed the presence of aberrant expansion alleles for 11 (31%). For seven of these patients the genotype was compatible with the phenotypic description, and resulted in a molecular diagnosis. We subsequently tested the remainder of our diagnostic ES cohort, including over 30 clinically and genetically heterogeneous disorders. Optimized manual curation yielded 140 samples with a likely aberrant STR length. Validations confirmed 70/140 (50%) aberrant expansion alleles, of which 48 were in the pathogenic range and 22 in the premutation range.ConclusionsOur work provides guidance for the implementation of STR analysis in clinical ES. Our results show that systematic STR evaluation may increase diagnostic ES yield by 0.2%, and recommend to make STR evaluation a routine part of ES interpretation in genetic testing laboratories.

scholarly journals Systematic analysis of short tandem repeats in 38,095 exomes provides an additional diagnostic yield

2021 ◽  
Author(s):  
Bart P. G. H. van der Sanden ◽  
Jordi Corominas ◽  
Michelle de Groot ◽  
Maartje Pennings ◽  
Rowdy P. P. Meijer ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Diagnostic Yield ◽  
Systematic Analysis ◽  
Short Tandem

scholarly journals Disputed paternity presumption in Burkina Faso: determination of the biological fathers of children using ABO-rhesus/hemoglobin electrophoresis and STR assays

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Missa Millogo ◽  
Serge Theophile Soubeiga ◽  
Bapio Valerie Jean Telesphore Bazie ◽  
Theodora Mahoukede Zohoncon ◽  
Abdoul Karim Ouattara ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Str Analysis ◽  
Resource Limited ◽  
Biological Fathers ◽  
Short Tandem

Abstract Background In resource-limited countries, ABO, HLA, MNS, Kells, and hemoglobin electrophoresis are classic tests for the resolution of paternity disputes due to their affordable cost. The limitations of these tests in cases of disputed paternity require the use of Short Tandem Repeats (STR) for their certification. This study aimed to determine the biological fathers of children using ABO-rhesus/hemoglobin electrophoresis and STR assays in Burkina Faso, West Africa. Results Of the fourteen trios studied, the ABO-rhesus/hemoglobin electrophoresis analysis revealed ten probable inclusion cases, three exclusion cases, and one undetermined paternity. DNA STR analysis found five inclusions of paternity out of the ten probable inclusions with ABO-rhesus/hemoglobin electrophoresis assay versus nine exclusions of paternity. Conclusion This study showed that the implementation of the analysis of short tandem repeat is required to resolve increasing disputed filiation cases in Burkina Faso.

scholarly journals Identification and Characterization of Nine Novel X-Chromosomal Short Tandem Repeats on Xp21.1, Xq21.31, and Xq23 Regions

2021 ◽  
Vol 12 ◽  
Author(s):  
Qinrui Yang ◽  
Jinglei Qian ◽  
Chengchen Shao ◽  
Yining Yao ◽  
Zhihan Zhou ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Mapping Function ◽  
Str Analysis ◽  
The Family ◽  
Further Development ◽  
Multiplex System ◽  
Short Tandem ◽  
Forensic Parameters

The application of X-chromosomal short tandem repeats (X-STRs) has been recognized as a powerful tool in complex kinship testing. To support further development of X-STR analysis in forensic use, we identified nine novel X-STRs, which could be clustered into three linkage groups on Xp21.1, Xq21.31, and Xq23. A multiplex PCR system was built based on the electrophoresis. A total of 198 unrelated Shanghai Han samples along with 168 samples from 43 families was collected to investigate the genetic polymorphism and forensic parameters of the nine loci. Allele numbers ranged from 5 to 12, and amplicon sizes ranged from 146 to 477 bp. The multiplex showed high values for the combined power of discrimination (0.99997977 in males and 0.99999999 in females) and combined mean exclusion chances (0.99997918 and 0.99997821 in trios, 0.99984939 in duos, and 0.99984200 in deficiency cases). The linkage between all pairs of loci was estimated via Kosambi mapping function and linkage disequilibrium test, and further investigated through the family study. The data from 43 families strongly demonstrated an independent transmission between LGs and a tight linkage among loci within the same LG. All these results support that the newly described X-STRs and the multiplex system are highly promising for further forensic use.

Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

1997 ◽  
Vol 45 (3) ◽  
pp. 265-270 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
Mark Seielstad ◽  
Eva Mateu ◽  
David Comas ◽  
...  
Keyword(s):  
Population Genetics ◽  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

Conditional Genotypic Probabilities for Microsatellite Loci

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1973-1980
Author(s):  
Jinko Graham ◽  
James Curran ◽  
B S Weir
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Dirichlet Distribution ◽  
Forensic Dna ◽  
Match Probability ◽  
Microsatellite Genotype ◽  
Allelic State ◽  
Forensic Assessments ◽  
Dna Profiles ◽  
Short Tandem

Abstract Modern forensic DNA profiles are constructed using microsatellites, short tandem repeats of 2–5 bases. In the absence of genetic data on a crime-specific subpopulation, one tool for evaluating profile evidence is the match probability. The match probability is the conditional probability that a random person would have the profile of interest given that the suspect has it and that these people are different members of the same subpopulation. One issue in evaluating the match probability is population differentiation, which can induce coancestry among subpopulation members. Forensic assessments that ignore coancestry typically overstate the strength of evidence against the suspect. Theory has been developed to account for coancestry; assumptions include a steady-state population and a mutation model in which the allelic state after a mutation event is independent of the prior state. Under these assumptions, the joint allelic probabilities within a subpopulation may be approximated by the moments of a Dirichlet distribution. We investigate the adequacy of this approximation for profiled loci that mutate according to a generalized stepwise model. Simulations suggest that the Dirichlet theory can still overstate the evidence against a suspect with a common microsatellite genotype. However, Dirichlet-based estimators were less biased than the product-rule estimator, which ignores coancestry.

scholarly journals Short Tandem Repeats Define a Gestational Origin for Metastatic Choriocarcinoma

2019 ◽  
Vol 108 (2) ◽  
pp. e115-e117
Author(s):  
Kelly Brown ◽  
Robert Homer ◽  
Marina Baine ◽  
Justin D. Blasberg
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem
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