scholarly journals Admixture Has Shaped Romani Genetic Diversity in Clinically Relevant Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Neus Font-Porterias ◽  
Aaron Giménez ◽  
Annabel Carballo-Mesa ◽  
Francesc Calafell ◽  
David Comas
Keyword(s):  
South Asian ◽  
Complex Traits ◽  
Genetic Disorders ◽  
Low Frequency ◽  
Population Variation ◽  
Minority Ethnic Group ◽  
Founder Mutations ◽  
Pathogenic Variants ◽  
Frequency Changes ◽  
Response Variation

Genetic patterns of inter-population variation are a result of different demographic and adaptive histories, which gradually shape the frequency distribution of the variants. However, the study of clinically relevant mutations has a Eurocentric bias. The Romani, the largest transnational minority ethnic group in Europe, originated in South Asia and received extensive gene flow from West Eurasia. Most medical genetic studies have only explored founder mutations related to Mendelian disorders in this population. Here we analyze exome sequences and genome-wide array data of 89 healthy Spanish Roma individuals to study complex traits and disease. We apply a different framework and focus on variants with both increased and decreased allele frequencies, taking into account their local ancestry. We report several OMIM traits enriched for genes with deleterious variants showing increased frequencies in Roma or in non-Roma (e.g., obesity is enriched in Roma, with an associated variant linked to South Asian ancestry; while non-insulin dependent diabetes is enriched in non-Roma Europeans). In addition, previously reported pathogenic variants also show differences among populations, where some variants segregating at low frequency in non-Roma are virtually absent in the Roma. Lastly, we describe frequency changes in drug-response variation, where many of the variants increased in Roma are clinically associated with metabolic and cardiovascular-related drugs. These results suggest that clinically relevant variation in Roma cannot only be characterized in terms of founder mutations. Instead, we observe frequency differences compared to non-Roma: some variants are absent, while other have drifted to higher frequencies. As a result of the admixture events, these clinically damaging variants can be traced back to both European and South Asian-related ancestries. This can be attributed to a different prevalence of some genetic disorders or to the fact that genetic susceptibility variants are mostly studied in populations of European descent, and can differ in individuals with different ancestries.

SEM image sharpness analysis

1996 ◽  
Vol 54 ◽  
pp. 142-143
Author(s):  
M. T. Postek ◽  
A. E. Vladar
Keyword(s):  
High Frequency ◽  
Low Frequency ◽  
Quantitative Information ◽  
Primary Electron ◽  
Image Sharpness ◽  
Critical Dimensions ◽  
Sem Image ◽  
Frequency Changes ◽  
Electron Microscopes ◽  
Scanning Electron

Fully automated or semi-automated scanning electron microscopes (SEM) are now commonly used in semiconductor production and other forms of manufacturing. The industry requires that an automated instrument must be routinely capable of 5 nm resolution (or better) at 1.0 kV accelerating voltage for the measurement of nominal 0.25-0.35 micrometer semiconductor critical dimensions. Testing and proving that the instrument is performing at this level on a day-by-day basis is an industry need and concern which has been the object of a study at NIST and the fundamentals and results are discussed in this paper.In scanning electron microscopy, two of the most important instrument parameters are the size and shape of the primary electron beam and any image taken in a scanning electron microscope is the result of the sample and electron probe interaction. The low frequency changes in the video signal, collected from the sample, contains information about the larger features and the high frequency changes carry information of finer details. The sharper the image, the larger the number of high frequency components making up that image. Fast Fourier Transform (FFT) analysis of an SEM image can be employed to provide qualitiative and ultimately quantitative information regarding the SEM image quality.

scholarly journals Current recommendations for clinical surveillance and genetic testing in rhabdoid tumor predisposition: a report from the SIOPE Host Genome Working Group

2021 ◽  
Author(s):  
M. C. Frühwald ◽  
K. Nemes ◽  
H. Boztug ◽  
M. C. A. Cornips ◽  
D. G. Evans ◽  
...  
Keyword(s):  
Working Group ◽  
Soft Part ◽  
Genetic Disorders ◽  
Panel Discussion ◽  
Rhabdoid Tumor ◽  
Host Genome ◽  
Cancer Surveillance ◽  
Malignant Neoplasms ◽  
Pathogenic Variants ◽  
Increased Risk

AbstractThe rhabdoid tumor (RT) predisposition syndromes 1 and 2 (RTPS1 and 2) are rare genetic conditions rendering young children vulnerable to an increased risk of RT, malignant neoplasms affecting the kidney, miscellaneous soft-part tissues, the liver and the central nervous system (Atypical Teratoid Rhabdoid Tumors, ATRT). Both, RTPS1&2 are due to pathogenic variants (PV) in genes encoding constituents of the BAF chromatin remodeling complex, i.e. SMARCB1 (RTPS1) and SMARCA4 (RTPS2). In contrast to other genetic disorders related to PVs in SMARCB1 and SMARCA4 such as Coffin-Siris Syndrome, RTPS1&2 are characterized by a predominance of truncating PVs, terminating transcription thus explaining a specific cancer risk. The penetrance of RTPS1 early in life is high and associated with a poor survival. However, few unaffected carriers may be encountered. Beyond RT, the tumor spectrum may be larger than initially suspected, and cancer surveillance offered to unaffected carriers (siblings or parents) and long-term survivors of RT is still a matter of discussion. RTPS2 exposes female carriers to an ill-defined risk of small cell carcinoma of the ovaries, hypercalcemic type (SCCOHT), which may appear in prepubertal females. RT surveillance protocols for these rare families have not been established. To address unresolved issues in the care of individuals with RTPS and to propose appropriate surveillance guidelines in childhood, the SIOPe Host Genome working group invited pediatric oncologists and geneticists to contribute to an expert meeting. The current manuscript summarizes conclusions of the panel discussion, including consented statements as well as non-evidence-based proposals for validation in the future.

scholarly journals A scalable EHR-based approach for phenotype discovery and variant interpretation for hereditary cancer genes

2021 ◽  
Author(s):  
Chenjie Zeng ◽  
Lisa A Bastarache ◽  
Ran Tao ◽  
Eric Venner ◽  
Scott Hebbring ◽  
...  
Keyword(s):  
Hereditary Cancer ◽  
Meta Analysis ◽  
Genetic Disorders ◽  
Genomic Medicine ◽  
Risk Scores ◽  
Cancer Genes ◽  
Pathogenic Variants ◽  
Emerge Network ◽  
Uncertain Significance ◽  
Potential Pathogenicity

Knowledge of the clinical spectrum of rare genetic disorders helps in disease management and variant pathogenicity interpretation. Leveraging electronic health record (EHR)-linked genetic testing data from the eMERGE network, we determined the associations between a set of 23 hereditary cancer genes and 3017 phenotypes in 23544 individuals. This phenome-wide association study replicated 45% (184/406) of known gene-phenotype associations (P = 5.1 ×10-125). Meta-analysis with an independent EHR-derived cohort of 3242 patients confirmed 14 novel associations with phenotypes in the neoplastic, genitourinary, digestive, congenital, metabolic, mental and neurologic categories. Phenotype risk scores (PheRS) based on weighted aggregations of EHR phenotypes accurately predicted variant pathogenicity for at least 50% of pathogenic variants for 8/23 genes. We generated a catalog of PheRS for 7800 variants, including 5217 variants of uncertain significance, to provide empirical evidence of potential pathogenicity. This study highlights the potential of EHR data in genomic medicine.

scholarly journals The evolving role of germline genetic testing and management in prostate cancer: Report from the Princess Margaret Cancer Centre International Retreat

2021 ◽  
Vol 15 (12) ◽  
Author(s):  
Roderick Clark ◽  
Miran Kenk ◽  
Kristen McAlpine ◽  
Emily Thain ◽  
Kirsten M. Farncombe ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Genetic Testing ◽  
Genetic Risk ◽  
Genetic Disorders ◽  
Future Research ◽  
Policy Action ◽  
Cancer Centre ◽  
Pathogenic Variants ◽  
Increased Risk ◽  
International Experts

Introduction: Prostate cancer is a significant cause of cancer mortality. It has been well-established that certain germline pathogenic variants confer both an increased risk of being diagnosed with prostate cancer and dying of prostate cancer.1 There are exciting developments in both the availability of genetic testing and opportunities for improved treatment of patients. On August 19, 2020, the Princess Margaret Cancer Centre in Toronto, Ontario, hosted a virtual retreat, bringing together international experts in urology, medical oncology, radiation oncology, medical genetics, and translational research, as well as a patient representative. We are pleased to provide this manuscript as a review of those proceedings for Canadian clinicians. Recommendations: We drafted several recommendations for future research and policy action based on this meeting: 1) Need for increased access to funding for germline testing for the common genetic disorders associated with increased risk of prostate cancer. 2) A need for increased research into identifying genetic factors influencing risk stratification, treatment response, and outcomes of prostate cancer within Canadian populations at increased genetic risk for prostate cancer. 3) Need for increased awareness about genetic risk factors among the Canadian public. 4) Need for research on patient perspectives and psychosocial outcomes in individuals identified to be at increased genetic risk of prostate cancer. 5) We support the creation of specialized multidisciplinary clinics that specialize in tailored care for patients at increased genetic risk of prostate cancer.

scholarly journals LeafCutter: annotation-free quantification of RNA splicing

2016 ◽  
Author(s):  
Yang I Li ◽  
David A Knowles ◽  
Jack Humphrey ◽  
Alvaro N. Barbeira ◽  
Scott P. Dickinson ◽  
...  
Keyword(s):  
Complex Traits ◽  
Rna Splicing ◽  
Population Variation ◽  
Disease Genes ◽  
Intron Splicing ◽  
Rna Seq ◽  
Exon Usage ◽  
Molecular Effects ◽  
Free Quantification ◽  
Gene Expression Levels

AbstractThe excision of introns from pre-mRNA is an essential step in mRNA processing. We developed LeafCutter to study sample and population variation in intron splicing. LeafCutter identifies variable intron splicing events from short-read RNA-seq data and finds alternative splicing events of high complexity. Our approach obviates the need for transcript annotations and circumvents the challenges in estimating relative isoform or exon usage in complex splicing events. LeafCutter can be used both for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). Compared to contemporary methods, we find 1.4–2.1 times more sQTLs, many of which help us ascribe molecular effects to disease-associated variants. Strikingly, transcriptome-wide associations between LeafCutter intron quantifications and 40 complex traits increased the number of associated disease genes at 5% FDR by an average of 2.1-fold as compared to using gene expression levels alone. LeafCutter is fast, scalable, easy to use, and available at https://github.com/davidaknowles/leafcutter.

Searching for genes in Schizophrenia

1999 ◽  
Vol 11 (2) ◽  
pp. 50-53 ◽  
Author(s):  
D.B. Wildenauer ◽  
S.G. Schwab ◽  
W. Maier ◽  
B. Lerer
Keyword(s):  
Genetic Variation ◽  
Human Genome Project ◽  
Complex Traits ◽  
Genetic Factors ◽  
Genetic Disorders ◽  
Genome Project ◽  
Turn Of The Century ◽  
Adoption Studies ◽  
Targeted Treatments ◽  
The Human Genome Project

Decades of research into the etiology of schizophrenia on a phenotypic level, i.e. studies of neuroanatomy, neuropathology, neurophysiology and other areas such as immunology have yielded only fragmentary results. A contribution of genetic factors, has been consistently shown, however, beginning with E. Kraepelin's pioneering studies at the turn of the century. Evidence has accumulated from family-, twin-, and adoption studies. Identical twins have a 48% risk of developing schizophrenia if one of them is affected. In contrast, a 17 % risk is reported for nonidentical twins. These rates are similar to other complex genetic disorders such as diabetes, hypertension and asthma. Advances in the genetic analysis of complex traits as well as progress in the Human Genome Project should provide a basis for uncovering the molecular causes of schizophrenic disorders and for investigating the neuropathology of this individually and socially devastating neuropsychiatrie disorder. There is no doubt, that discovery of the genetic variation associated with the illness would help in identifying specific targets for development of more effective, targeted treatments.

scholarly journals Assessing Lysosomal Disorders in the NGS Era: Identification of Novel Rare Variants

2020 ◽  
Vol 21 (17) ◽  
pp. 6355
Author(s):  
Marisa Encarnação ◽  
Maria Francisca Coutinho ◽  
Lisbeth Silva ◽  
Diogo Ribeiro ◽  
Souad Ouesleti ◽  
...  
Keyword(s):  
Rare Variants ◽  
Health Care Systems ◽  
Genetic Disorders ◽  
Case Series ◽  
In Silico Analysis ◽  
Analysis Data ◽  
Lysosomal Storage ◽  
Pathogenic Variants ◽  
Number Of Patients

Lysosomal storage diseases (LSDs) are a heterogeneous group of genetic disorders with variable degrees of severity and a broad phenotypic spectrum, which may overlap with a number of other conditions. While individually rare, as a group LSDs affect a significant number of patients, placing an important burden on affected individuals and their families but also on national health care systems worldwide. Here, we present our results on the use of an in-house customized next-generation sequencing (NGS) panel of genes related to lysosome function as a first-line molecular test for the diagnosis of LSDs. Ultimately, our goal is to provide a fast and effective tool to screen for virtually all LSDs in a single run, thus contributing to decrease the diagnostic odyssey, accelerating the time to diagnosis. Our study enrolled a group of 23 patients with variable degrees of clinical and/or biochemical suspicion of LSD. Briefly, NGS analysis data workflow, followed by segregation analysis allowed the characterization of approximately 41% of the analyzed patients and the identification of 10 different pathogenic variants, underlying nine LSDs. Importantly, four of those variants were novel, and, when applicable, their effect over protein structure was evaluated through in silico analysis. One of the novel pathogenic variants was identified in the GM2A gene, which is associated with an ultra-rare (or misdiagnosed) LSD, the AB variant of GM2 Gangliosidosis. Overall, this case series highlights not only the major advantages of NGS-based diagnostic approaches but also, to some extent, its limitations ultimately promoting a reflection on the role of targeted panels as a primary tool for the prompt characterization of LSD patients.

Dynamic modulation of cerebrovascular resistance as an index of autoregulation under tilt and controlled Pet CO2

2002 ◽  
Vol 283 (3) ◽  
pp. R653-R662 ◽  
Author(s):  
Michael R. Edwards ◽  
J. Kevin Shoemaker ◽  
Richard L. Hughson
Keyword(s):  
Transfer Function ◽  
Function Analysis ◽  
Low Frequency ◽  
Mean Flow ◽  
Low Frequencies ◽  
Cerebrovascular Autoregulation ◽  
Cerebrovascular Resistance ◽  
Arterial Blood ◽  
Transfer Function Analysis ◽  
Frequency Changes

Transfer function analysis of the arterial blood pressure (BP)-mean flow velocity (MFV) relationship describes an aspect of cerebrovascular autoregulation. We hypothesized that the transfer function relating BP to cerebrovascular resistance (CVRi) would be sensitive to low-frequency changes in autoregulation induced by head-up tilt (HUT) and altered arterial Pco 2. Nine subjects were studied in supine and HUT positions with end-tidal Pco 2(Pet CO2 ) kept constant at normal levels: +5 and −5 mmHg. The BP-MFV relationship had low coherence at low frequencies, and there were significant effects of HUT on gain only at high frequencies and of Pco 2 on phase only at low frequencies. BP → CVRi had coherence >0.5 from very low to low frequencies. There was a significant reduction of gain with increased Pco 2 in the very low and low frequencies and with HUT at the low frequency. Phase was affected by Pco 2 in the very low frequencies. Transfer function analysis of BP → CVRi provides direct evidence of altered cerebrovascular autoregulation under HUT and higher levels of Pco 2.

scholarly journals A large deletion in the COL2A1 gene expands the spectrum of pathogenic variants causing bulldog calf syndrome in cattle

2020 ◽  
Vol 62 (1) ◽  
Author(s):  
Joana Gonçalves Pontes Jacinto ◽  
Irene Monika Häfliger ◽  
Anna Letko ◽  
Cord Drögemüller ◽  
Jørgen Steen Agerholm
Keyword(s):  
De Novo ◽  
Genetic Disorders ◽  
Polymerase Chain Reaction Analysis ◽  
Large Deletion ◽  
Whole Genome Sequence ◽  
De Novo Mutation ◽  
Loss Of Function ◽  
Single Nucleotide Variants ◽  
Pathogenic Variants ◽  
Base Pair Deletion

Abstract Background Congenital bovine chondrodysplasia, also known as bulldog calf syndrome, is characterized by disproportionate growth of bones resulting in a shortened and compressed body, mainly due to reduced length of the spine and the long bones of the limbs. In addition, severe facial dysmorphisms including palatoschisis and shortening of the viscerocranium are present. Abnormalities in the gene collagen type II alpha 1 chain (COL2A1) have been associated with some cases of the bulldog calf syndrome. Until now, six pathogenic single-nucleotide variants have been found in COL2A1. Here we present a novel variant in COL2A1 of a Holstein calf and provide an overview of the phenotypic and allelic heterogeneity of the COL2A1-related bulldog calf syndrome in cattle. Case presentation The calf was aborted at gestation day 264 and showed generalized disproportionate dwarfism, with a shortened compressed body and limbs, and dysplasia of the viscerocranium; a phenotype resembling bulldog calf syndrome due to an abnormality in COL2A1. Whole-genome sequence (WGS) data was obtained and revealed a heterozygous 3513 base pair deletion encompassing 10 of the 54 coding exons of COL2A1. Polymerase chain reaction analysis and Sanger sequencing confirmed the breakpoints of the deletion and its absence in the genomes of both parents. Conclusions The pathological and genetic findings were consistent with a case of “bulldog calf syndrome”. The identified variant causing the syndrome was the result of a de novo mutation event that either occurred post-zygotically in the developing embryo or was inherited because of low-level mosaicism in one of the parents. The identified loss-of-function variant is pathogenic due to COL2A1 haploinsufficiency and represents the first structural variant causing bulldog calf syndrome in cattle. Furthermore, this case report highlights the utility of WGS-based precise diagnostics for understanding congenital disorders in cattle and the need for continued surveillance for genetic disorders in cattle.

Sign in / Sign up

Export Citation Format

Share Document