The Genetics Institute
The Genetics Institute
Volodarsky M.,Ben - Gurion University of the Negev |
Markus B.,Ben - Gurion University of the Negev |
Cohen I.,Ben - Gurion University of the Negev |
Staretz-Chacham O.,Soroka Medical Center |
And 7 more authors.
Human Mutation | Year: 2013
Autosomal recessive osteogenesis imperfecta (OI) was diagnosed in three unrelated Israeli Bedouin consanguineous families. Fractures were evident in all cases in infancy. Genome-wide linkage analysis ruled out association with any of the known OI genes, and identified a single homozygosity locus of approximately 2 Mb on chromosome 9 common to all affected individuals (maximum multipoint lod score 6.5). Whole exome sequencing identified only a single mutation within this locus that was shared by all affected individuals: a homozygous deletion mutation of exon 4 of TMEM38B, leading to an early stop codon and a truncated protein, as well as low TMEM38B mRNA levels. TMEM38B encodes TRIC-B, a ubiquitous component of TRIC, a monovalent cation-specific channel involved in Ca2+ release from intracellular stores that has been shown to act in cell differentiation. Molecular mechanisms through which a TMEM38B mutation might lead to an OI phenotype are yet to be explored. We demonstrate through homozygosity mapping and whole exome seuquencing that autosomal recessive osteogensis imperfecta (OI) type IV is associated with a homozygous deletion mutation of exon 4 of TMEM38B. TMEM38B encodes TRIC-B, a ubiquitous component of TRIC, a monovalent cation-specific channel involved in Ca2+ release from intracellular stores that has been shown to act in cell differentiation. © 2013 Wiley Periodicals, Inc.
PubMed | The Genetics Institute, Beilinson Hospital, Hebrew University of Jerusalem, Tel-Hai Academic College and 6 more.
Type: Journal Article | Journal: Pediatric blood & cancer | Year: 2016
Heterozygous germline mutations in any of the mismatch repair (MMR) genes, MLH1, MSH2, MSH6, and PMS2, cause Lynch syndrome (LS), an autosomal dominant cancer predisposition syndrome conferring a high risk of colorectal, endometrial, and other cancers in adulthood. Offspring of couples where both spouses have LS have a 1:4 risk of inheriting biallelic MMR gene mutations. These cause constitutional MMR deficiency (CMMRD) syndrome, a severe recessively inherited cancer syndrome with a broad tumor spectrum including mainly hematological malignancies, brain tumors, and colon cancer in childhood and adolescence. Many CMMRD children also present with caf au lait spots and axillary freckling mimicking neurofibromatosis type 1.We describe our experience in seven CMMRD families demonstrating the role and importance of founder mutations and consanguinity on its prevalence. Clinical presentations included brain tumors, colon cancer, lymphoma, and small bowel cancer.In children from two nonconsanguineous Ashkenazi Jewish (AJ) families, the common Ashkenazi founder mutations were detected; these were homozygous in one family and compound heterozygous in the other. In four consanguineous families of various ancestries, different homozygous mutations were identified. In a nonconsanguineous Caucasus/AJ family, lack of PMS2 was demonstrated in tumor and normal tissues; however, mutations were not identified.CMMRD is rare, but, especially in areas where founder mutations for LS and consanguinity are common, pediatricians should be aware of it since they are the first to encounter these children. Early diagnosis will enable tailored cancer surveillance in the entire family and a discussion regarding prenatal genetic diagnosis.
PubMed | The Oncology Institute Sheba Medical Center, Beilinson Hospital, Hebrew University of Jerusalem, Institute of Oncology and 8 more.
Type: Journal Article | Journal: Breast cancer research and treatment | Year: 2016
We evaluated the clinical utility of screening for mutations in 34 breast/ovarian cancer susceptibility genes in high-risk families in Israel. Participants were recruited from 12, 2012 to 6, 2015 from 8 medical centers. All participants had high breast/ovarian cancer risk based on personal and family history. Genotyping was performed with the InVitae platform. The study was approved by the ethics committees of the participating centers; all participants gave a written informed consent before entering the study. Overall, 282 individuals participated in the study: 149 (53%) of Ashkenazi descent, 80 (28%) Jewish non-Ashkenazi descent, 22 (8%) of mixed Ashkenazi/non-Ashkenazi origin, 21 (7%) were non-Jewish Caucasians, and the remaining patients (n=10-3.5%) were of Christian Arabs/Druze/unknown ethnicity. For breast cancer patients (n=165), the median (range) age at diagnosis was 46 (22-90) years and for ovarian cancer (n=15) 54 (38-69) years. Overall, 30 cases (10.6%) were found to carry a pathogenic actionable mutation in the tested genes: 10 BRCA1 (3 non-founder mutations), 9 BRCA2 (8 non-founder mutations), and one each in the RAD51C and CHEK2 genes. Furthermore, actionable mutations were detected in 9 more cases in 4 additional genes (MSH2, RET, MSH6, and APC). No pathogenic mutations were detected in the other genotyped genes. In this high-risk population, 10.6% harbored an actionable pathogenic mutation, including non-founder mutations in BRCA1/2 and in additional cancer susceptibility genes, suggesting that high-risk families should be genotyped and be assigned a genotype-based cancer risk.
PubMed | The Genetics Institute, Beilinson Hospital, Genetics Unit, Rabin Medical Center and 3 more.
Type: Journal Article | Journal: American journal of medical genetics. Part A | Year: 2016
One of the goals of evaluating a patient in the genetics clinic is to find the diagnosis that would explain his or her clinical presentation. Sometimes the patients diagnosis remains undefined or does not explain all of the clinical findings. As clinicians are often guided by a single disorder paradigm, diagnosing multiple genetic conditions in the same patient requires a heightened sense of awareness. Over the last few years, we evaluated several patients (n=14) who were found to have more than one genetic diagnosis. In this paper, we will describe their natural history and diagnoses, and draw on the lessons learned from this phenomenon, which we expect to grow in this era of next-generation diagnostic technologies. To our knowledge, this is by far the largest series of patients with double diagnoses. Based on our findings, we strongly recommend that physicians question every diagnosis to determine whether it indeed explains all of the patients symptoms, and consider whether they should continue the diagnostic evaluation to look for a more accurate and complete set of diagnoses. 2016 Wiley Periodicals, Inc.
PubMed | The Genetics Institute, Central Laboratory, Pathology Institute, Meir Medical Center and Assaf Harofeh Medical Center
Type: Journal Article | Journal: Archives of gynecology and obstetrics | Year: 2016
The use of maternal serum alpha fetoprotein (MSAFP) levels as a predictor of pregnancy complications (PC) is well established. We hypothesized that the ratio between the MSAFP/AFAFP levels (RATIO) will more accurately predict PC than MSAFP levels alone.Women who had a MSAFP test followed by amniocentesis were divided into two groups: those who had PC comprised the study group and those who had an uneventful pregnancy served as the control group. Data regarding pregnancy and delivery course were collected. The RATIO between the study and the control groups was compared.166 women were included in the study, of which 24 had PC. A significant correlation was found between the RATIO and intrauterine growth restriction (IUGR) and week of delivery. Six pregnancies had elevated MSAFP levels; two with RATIO below 2 had uneventful pregnancies. Among the other four pregnancies with RATIO above two, one had IUGR and the other, placental abruption.Our data suggest that the RATIO might serve as a predictor of IUGR and week of delivery. Although the number of patients in the current study was relatively small, the novelty of the proposed simple marker implies that a larger scale study is warranted. Such studies may confirm this finding and a possible advantage of using this RATIO instead of or in addition to MSAFP values for better prediction of pregnancies at risk for PC.
Markus B.,Ben - Gurion University of the Negev |
Birk O.S.,Ben - Gurion University of the Negev |
Birk O.S.,The Genetics Institute |
Geiger D.,Technion - Israel Institute of Technology
Bioinformatics | Year: 2011
Motivation: High-throughput single nucleotide polymorphism (SNP) arrays have become the standard platform for linkage and association analyses. The high SNP density of these platforms allows high-resolution identification of ancestral recombination events even for distant relatives many generations apart. However, such inference is sensitive to marker mistyping and current error detection methods rely on the genotyping of additional close relatives. Genotyping algorithms provide a confidence score for each marker call that is currently not integrated in existing methods. There is a need for a model that incorporates this prior information within the standard identical by descent (IBD) and association analyses. Results: We propose a novel model that incorporates marker confidence scores within IBD methods based on the Lander-Green Hidden Markov Model. The novel parameter of this model is the joint distribution of confidence scores and error status per array. We estimate this probability distribution by applying a modified expectation-maximization (EM) procedure on data from nuclear families genotyped with Affymetrix 250K SNP arrays. The converged tables from two different genotyping algorithms are shown for a wide range of error rates. We demonstrate the efficacy of our method in refining the detection of IBD signals using nuclear pedigrees and distant relatives. © The Author 2011. Published by Oxford University Press. All rights reserved.
PubMed | The Genetics Institute and Tel Aviv University
Type: | Journal: Blood cells, molecules & diseases | Year: 2016
Bone crises in type 1 Gaucher disease are reported in long bones and occasionally in weight bearing bones and other bones, but rarely in small bones of the hands and feet. We retrospectively examined the incidence of bone pain in patients followed at the Rabin Medical Center, Israel, before and following the initiation of enzyme replacement therapy (ERT) and evaluated them for bone crises. Of 100 type I Gaucher disease patients, 30 (30%) experienced one or more bone crises. Small bone crises represented 31.5% of all bone crises and were always preceded by crises in other bones. While the incidence of long bone crises reduced after the initiation of ERT, small bone crises increased. Almost 60% of patients with bone crises were of the N370S/84GG genotype suggesting a greater susceptibility of N370S/84GG patients to severe bone complications. These patients also underwent the greatest number of splenectomies (70.6% of splenectomised patients). Splenectomised patients showed a trend towards increased long and small bone crises after surgery. Active investigation of acute pain in the hands and feet in patients in our cohort has revealed a high incidence of small bone crises. Physicians should consider imaging studies to investigate unexplained pain in these areas.
PubMed | The Genetics Institute and Ben - Gurion University of the Negev
Type: Journal Article | Journal: Heredity | Year: 2014
The Bedouin Israeli population is highly inbred and structured with a very high prevalence of recessive diseases. Many studies in the past two decades focused on linkage analysis in large, multiple consanguineous pedigrees of this population. The advent of high-throughput technologies motivated researchers to search for rare variants shared between smaller pedigrees, integrating data from clinically similar yet seemingly non-related sporadic cases. However, such analyses are challenging because, without pedigree data, there is no prior knowledge regarding possible relatedness between the sporadic cases. Here, we describe models and techniques for the study of relationships between pedigrees and use them for the inference of tribal co-ancestry, delineating the complex social interactions between different tribes in the Negev Bedouins of southern Israel. Through our analysis, we differentiate between tribes that share many yet small genomic segments because of co-ancestry versus tribes that share larger segments because of recent admixture. The emergent pattern is well correlated with the prevalence of rare mutations in the different tribes. Tribes that do not intermarry, mostly because of social restrictions, hold private mutations, whereas tribes that do intermarry demonstrate a genetic flow of mutations between them. Thus, social structure within an inbred community can be delineated through genomic data, with implications to genetic counseling and genetic mapping.
PubMed | The Genetics Institute, Beilinson Hospital and Bioinformatics Unit Sheba Cancer Research Center
Type: | Journal: Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology | Year: 2017
An association between isolated, increased nuchal translucency thickness and pathogenic chromosomal microarray analysis (CMA) has been reported. A recent meta-analysis reported that most studies used a 3.5mm cut-off value. Considering nuchal translucency distribution and the commonly accepted 5% false positive rate in maternal serum screening, nuchal translucency cut-off levels should be reconsidered. This study evaluated the unique contribution of CMA to the investigation of foetuses with mildly increased nuchal translucency (NT) thickness of 3.0-3.4mm.This was a retrospective, multicenter study. A single laboratory performed all genetic analyses. Comparative Genomic Hybridization Microarray analysis or Single Nucleotide Polymorphism Array technology was used for CMA. NT was divided into three groups (2.9; 3.0-3.4; 3.5mm) and the results were compared, focusing on pregnancies with NT as the only medical indication for CMA at the time of the invasive procedure. If combined first trimester screening (NT and biochemistry) indicated increased risk for common aneuploidies, the case was excluded.CMA results were recorded in 1,588 pregnancies, of which 770 foetuses had NT as a normal or an isolated abnormal finding. Of these, 462 had NT 2.9mm, 170 had NT 3.0-3.4mm and 138 had NT 3.5mm. Pathogenic copy number variations were found in 1.7%, 7.1%, and 13.0%, respectively.The results suggest that CMA should be part of the investigation in foetuses with isolated, mildly increased NT (3.0-3.4mm).
Shalev S.A.,The Genetics Institute
Harefuah | Year: 2010
The principle deeds of genetics in Israel consist of a wide array of disciplines including agriculture, nutrients, biotechnology, pharmacology and pharmacogenetics, pertaining to criminal as well as medical aspects. In the scope of this state of the art historical review, the authors emphasize the medical issues. The initial stimulus for genetic studies and medical awareness among the various ethnic populations in Israel was the immigration, in the early 1950s, of over a million Jewish immigrants from more than 100 countries from all continents. It was soon recognized that frequencies of genetic diseases differed markedly among the various communities, serving as a trigger for studying and managing these populations. In this state of the art historical review, particular emphasize was given to the historical events concerning genetics in the land of Israel, as well as in the state of Israel. Highlights of genetic diversity of the various ethnic and sub-populations are added, along with the advances and major achievements of the human genetics discipline in the state of Israel.