Complete Paternal Uniparental Disomy of Chromosome 2 in an Asian Female Identified by Short Tandem Repeats and Whole Genome Sequencing

2019 ◽  
Vol 157 (4) ◽  
pp. 197-202 ◽  
Author(s):  
Xiaochuan Zhang ◽  
Zhaojun Ding ◽  
Ruwen He ◽  
Jiying Qi ◽  
Zijun Zhang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Uniparental Disomy ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Rare Type ◽  
Short Tandem Repeat Markers ◽  
Short Tandem

Uniparental disomy (UPD) is a rare type of chromosomal aberration that has sometimes been detected in paternity testing. We examined a 3-person family (father, mother, daughter) first by using short tandem repeat markers, which revealed 4 markers, TPOX, D2S1338, D2S1772, and D2S441, on chromosome 2 that were not transmitted in a Mendelian style. We then performed whole genome sequencing (WGS) to determine the range of the UPD. Chromosome 2 in the daughter showed a complete paternal UPD. To the best of our knowledge, this is the 4th case of complete paternal UPD of chromosome 2 with no clinical phenotype. Our study suggests that WGS, when performed to enhance the accuracy and reliability of parentage testing, can provide a powerful method to detect an UPD.

scholarly journals Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population

Heliyon ◽  
2018 ◽  
Vol 4 (5) ◽  
pp. e00625
Author(s):  
Satoshi Hirata ◽  
Kaname Kojima ◽  
Kazuharu Misawa ◽  
Olivier Gervais ◽  
Yosuke Kawai ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Japanese Population ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Whole Genome ◽  
Population Scale ◽  
Short Tandem

scholarly journals Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting

2020 ◽  
Vol 148 ◽  
Author(s):  
J. L. Guthrie ◽  
L. Strudwick ◽  
B. Roberts ◽  
M. Allen ◽  
J. McFadzen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Variable Number ◽  
Yukon Territory ◽  
Contact Tracing ◽  
Whole Genome ◽  
Attitudes And Practices ◽  
Genomic Epidemiology ◽  
Recent Transmission

Abstract Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005–2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.

scholarly journals Whole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden

2019 ◽  
Vol 7 (10) ◽  
pp. 398 ◽  
Author(s):  
Sacchini ◽  
Wahab ◽  
Di Giannatale ◽  
Zilli ◽  
Abass ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Brucella Melitensis ◽  
Geographic Origin ◽  
Variable Number ◽  
Human Brucellosis ◽  
Whole Genome ◽  
Multiple Loci ◽  
Imported Cases

Human infections with Brucella melitensis are occasionally reported in Sweden, despite the fact that the national flocks of sheep and goats are officially free from brucellosis. The aim of our study was to analyze 103 isolates of B. melitensis collected from patients in Sweden between 1994 and 2016 and determine their putative geographic origin using whole genome sequencing (WGS)-based tools. The majority of the strains were assigned to East Mediterranean and African lineages. Both in silico Multiple Loci VNTR (Variable Number of Tandem Repeats) Analysis (MLVA) and core genome Multilocus Sequence Typing (cgMLST) analyses identified countries of the Middle East as the most probable source of origin of the majority of the strains. Isolates collected from patients with travel history to Iraq or Syria were often associated with genotypes from Turkey, as the cgMLST profiles from these countries clustered together. Sixty strains were located within a distance of 20 core genes to related genotypes from the publicly available database, and for eighteen isolates, the closest genotype was different by more than 50 loci. Our study showed that WGS based tools are effective in tracing back the geographic origin of infection of patients with unknown travel status, provided that public sequences from the location of the source are available.

scholarly journals Body temperature predicts maximum microsatellite length in mammals

2008 ◽  
Vol 4 (4) ◽  
pp. 399-401 ◽  
Author(s):  
William Amos ◽  
Andrew Clarke
Keyword(s):  
Body Temperature ◽  
Genome Sequencing ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Temperature Dependent ◽  
Repeat Number ◽  
Stability Threshold ◽  
Marker Loci ◽  
Microsatellite Evolution ◽  
Short Tandem

A long-standing mystery in genome evolution is why short tandem repeats vary so much in length and frequency. Here, we test the hypothesis that body temperature acts to influence the rate and nature of slippage-based mutations. Using the data from both 28 species where genome sequencing is advanced and 76 species from which marker loci have been published, we show that in mammals, maximum repeat number is inversely correlated with body temperature, with warmer-blooded species having shorter ‘long’ microsatellites. Our results support a model of microsatellite evolution in which maximum length is limited by a temperature-dependent stability threshold.

scholarly journals Whole-genome sequencing suggests a role of MIF in the pathophysiology of TEMPI syndrome

2021 ◽  
Vol 5 (12) ◽  
pp. 2563-2568
Author(s):  
Chunyan Sun ◽  
Jian Xu ◽  
Bo Zhang ◽  
Haifan Huang ◽  
Lei Chen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Plasma Cells ◽  
Whole Genome ◽  
Chromosome 2 ◽  
Single Nucleotide Variants ◽  
Intrapulmonary Shunting ◽  
Complex Structural ◽  
Fluid Collections

TEMPI syndrome (telangiectasias, elevated erythropoietin level and erythrocytosis, monoclonal gammopathy, perinephric fluid collections, and intrapulmonary shunting) is a newly defined multisystemic disease with its pathophysiology largely unknown. Here, we report the whole-genome sequencing (WGS) analysis on the tumor-normal paired cells from a patient with TEMPI syndrome. WGS revealed somatic nonsynonymous single-nucleotide variants, including SLC7A8, NRP2, and AQP7. Complex structural variants of chromosome 2 were found, particularly within regions where some putative oncogenes reside. Of potential clinical relevance, duplication of 22q11.23 was identified, and the expression of the located gene macrophage migration inhibitory factor (MIF) was significantly upregulated in 3 patients with TEMPI syndrome. Importantly, the level of serum MIF in one patient with TEMPI syndrome was significantly decreased in accordance with the downtrend of plasma cells, M-protein, hemoglobin, and erythropoietin and the improvement of telangiectasias, perinephric fluid collections, and intrapulmonary shunting after treatment with plasma cell–directed therapy. In conclusion, our study provides insights into the genomic landscape and suggests a role of MIF in the pathophysiology of TEMPI syndrome.

scholarly journals Identification of Rice Large Grain Gene GW2 by Whole-Genome Sequencing of a Large Grain-Isogenic Line Integrated with Japonica Native Gene and Its Linkage Relationship with the Co-integrated Semidwarf Gene d60 on Chromosome 2

2019 ◽  
Vol 20 (21) ◽  
pp. 5442
Author(s):  
Motonori Tomita ◽  
Shiho Yazawa ◽  
Yoshimasa Uenishi
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rice Variety ◽  
Kernel Weight ◽  
Snp Markers ◽  
Recurrent Parent ◽  
Whole Genome ◽  
Isogenic Line ◽  
Chromosome 2 ◽  
Single Nucleotide

Genetic analysis of “InochinoIchi,” an exceptionally large grain rice variety, was conducted through five continuous backcrosses with Koshihikari as a recurrent parent using the large grain F3 plant in Koshihikari × Inochinoichi as a nonrecurrent parent. Thorough the F2 and all BCnF2 generations, large, medium, and small grain segregated in a 1:2:1 ratio, indicating that the large grain is controlled by a single allele. Mapping by using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers with small grain homozygous segregants in the F2 of Nipponbare × Inochinoichi, revealed linkage with around 7.7 Mb markers from the distal end of the short arm of chromosome 2. Whole-genome sequencing on a large grain isogenic Koshihikari (BC4F2) using next-generation sequencing (NGS) identified a single nucleotide deletion in GW2 gene, which is located 8.1 Mb from the end of chromosome 2, encoding a RING protein with E3 ubiquitin ligase activity. The GW2-integrated isogenic Koshihikari showed a 34% increase in thousand kernel weight compared to Koshihikari, while retaining a taste score of 80. We further developed a large grain/semi-dwarf isogenic Koshihikari integrated with GW2 and the semidwarfing gene d60, which was found to be localized on chromosome 2. The combined genotype secured high yielding while providing robustness to withstand climate change, which can contribute to the New Green Revolution.

scholarly journals The Brazilian Rare Genomes Project: validation of whole genome sequencing for rare diseases diagnosis

2021 ◽  
Author(s):  
Antonio Victor Campos Coelho ◽  
Bruna Mascaro Cordeiro de Azevedo ◽  
Danielle Ribeiro Lucon ◽  
Maria Soares Nobrega ◽  
Rodrigo de Souza Reis ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rare Diseases ◽  
Clinical Laboratory ◽  
Genomic Medicine ◽  
Uniparental Disomy ◽  
Public Healthcare ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
F Measure

Rare diseases affect 3.2 to 13.2 million individuals in Brazil. The Brazilian Rare Genomes Project is envisioned to further the implementation of genomic medicine into the Brazilian public healthcare system. Here we report the results of the validation of a whole genome sequencing (WGS) procedure for implementation in a clinical laboratory. In addition, we report data quality for the first 1,200 real world patients sequenced. For the validation, we sequenced a well characterized group of 76 samples, including seven gold standard genomes, using a PCR-free WGS protocol on Illumina Novaseq 6000 equipment. We compared the observed variant calls with their expected calls, observing good concordance for single nucleotide variants (SNVs; mean F-measure = 99.82%) and indels (mean F-measure = 99.57%). Copy number variants and structural variants events detection performances were as expected (F-measures 96.6% and 90.3%, respectively). Our protocol presented excellent intra- and inter-assay reproducibility, with coefficients of variation ranging between 0.03% and 0.20% and 0.02% and 0.09%, respectively. Limitations of the procedure include the inability to confidently detect variants such as uniparental disomy, balanced translocations, repeat expansion variants and low-level mosaicism. In summary, the observed performance of the test was in accordance with that seen in the best centers worldwide. The Rare Genomes Project is an important initiative to improve Brazil's general population access to the innovative WGS technology which has the potential to reduce the time until diagnosis of rare diseases, bringing pivotal improvements for the quality of life of the affected individuals.

Sign in / Sign up

Export Citation Format

Share Document