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Clinical Genetics

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https://www.readbyqxmd.com/read/29220073/collective-effects-of-common-snps-and-genetic-risk-prediction-in-type-1-diabetes
#1
Y Gui, X Lei, S Huang
Type 1 diabetes (T1D) is a common autoimmune disease and may be related to multiple genetic and environmental risk factors. Previous genetic studies have focused on looking for individual polymorphic risk variants. Here we studied the overall levels of genetic diversity in T1D patients by making use of a previously published study including 1,865 cases and 2,828 reference samples with genotyping data for 500K common single nucleotide polymorphisms (SNPs). We determined the minor allele status of each SNP in the reference samples and calculated the total number of minor alleles or minor allele contents (MAC) of each individual...
December 8, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29206279/the-risk-of-breast-cancer-in-brca1-and-brca2-mutation-carriers-without-a-first-degree-relative-with-breast-cancer
#2
K A Metcalfe, J Lubinski, J Gronwald, T Huzarski, J McCuaig, H T Lynch, B Karlan, W D Foulkes, C F Singer, S L Neuhausen, L Senter, A Eisen, P Sun, S A Narod
The objective of this study was to estimate the lifetime risk of breast cancer in women with a BRCA1 or BRCA2 mutation with and without at least one first-degree relative with breast cancer. A total of 2835 women with a BRCA1 or BRCA2 mutation were followed. Age- and gene-specific breast cancer rates were calculated. The relative risks of breast cancer for subjects with a family history of breast cancer, compared to no family history were calculated. The mean age at baseline was 41.1 years, and they were followed for a mean of 6...
December 5, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29206278/clinical-sequencing-from-raw-data-to-diagnosis-with-lifetime-value
#3
REVIEW
S M Caspar, N Dubacher, A M Kopps, J Meienberg, C Henggeler, G Matyas
High-throughput sequencing (HTS) has revolutionized genetics by enabling the detection of sequence variants at hitherto unprecedented large scale. Despite these advances, however, there are still remaining challenges in the complete coverage of targeted regions (genes, exome or genome) as well as in HTS data analysis and interpretation. Moreover, it is easy to get overwhelmed by the plethora of available methods and tools for HTS. Here, we review the step-by-step process from the generation of sequence data to molecular diagnosis of Mendelian diseases...
December 5, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29205322/a-targeted-sequencing-panel-identifies-rare-damaging-variants-in-multiple-genes-in-the-cranial-neural-tube-defect-anencephaly
#4
M Ishida, T Cullup, C Boustred, C James, J Docker, C English, GOSgene, N Lench, A J Copp, G E Moore, N D E Greene, P Stanier
Neural tube defects (NTDs) affecting the brain (anencephaly) are lethal before or at birth, whereas lower spinal defects (spina bifida) may lead to life-long neurological handicap. Collectively NTDs rank among the most common birth defects worldwide. This study focuses on anencephaly, which despite having a similar frequency to spina bifida and being the most common type of NTD observed in mouse models, has had more limited inclusion in genetic studies. A genetic influence is strongly implicated in determining risk of NTDs and a molecular diagnosis is of fundamental importance to families both in terms of understanding the origin of the condition and for managing future pregnancies...
December 4, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29194587/genetic-association-of-molecular-traits-a-help-to-identify-causative-variants-in-complex-diseases
#5
REVIEW
C Vandiedonck
In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies (GWAS). The genetic variants that modulate them are called expression quantitative trait loci (eQTL). Their study has been extended to other molecular quantitative trait loci (molQTL) that regulate gene expression at the various levels, from chromatin state to cellular responses...
December 1, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29194620/pharmacogenetics-a-strategy-for-personalized-medicine-for-autoimmune-diseases
#6
REVIEW
S Tavakolpour, M Darvishi, M Ghasemiadl
For many years, a considerable number of patients with autoimmune diseases (ADs) have suffered from a lack of drug response and drug-related toxicity. Despite the emergence of new therapeutic options such as biological agents, patients continue to struggle with these problems. Unfortunately, new challenges, including the paradoxical effects of biological drugs, have complicated the situation. In recent decades, efforts have been made to predict drug response as well as drug-related side-effects. Thanks to the many advances in genetics, evaluation of markers to predict drug response/toxicity before the initiation of treatment may be an avenue toward personalizing treatments...
November 30, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29194579/targeted-gene-sequencing-and-whole-exome-sequencing-in-autopsied-fetuses-with-prenatally-diagnosed-kidney-anomalies
#7
M Rasmussen, L Sunde, M L Nielsen, M Ramsing, A Petersen, T D Hjortshøj, T E Olsen, A Tabor, J M Hertz, I Johnsen, L Sperling, O B Petersen, U B Jensen, F G Møller, M B Petersen, D L Lildballe
Identification of fetal kidney anomalies invites questions about underlying causes and recurrence risk in future pregnancies. We therefore investigated the diagnostic yield of next-generation sequencing in fetuses with bilateral kidney anomalies and the correlation between disrupted genes and fetal phenotypes. Fetuses with bilateral kidney anomalies were screened using an in-house-designed kidney-gene panel. In families where candidate variants were not identified, whole-exome sequencing was performed. Genes uncovered by this analysis were added to our kidney-panel...
November 30, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29193034/hypermanganesemia-with-dystonia-polycythemia-and-cirrhosis-in-10-patients-six-novel-slc30a10-mutations-and-further-phenotype-delineation
#8
M S Zaki, M Y Issa, H M Elbendary, H El-Karaksy, H Hosny, C Ghobrial, A El Safty, A El-Hennawy, A Oraby, L Selim, M S Abdel-Hamid
Biallelic mutations in the SLC30A10 gene cause an inborn error of Mn metabolism characterized by hypermanganesemia, polycythemia, early-onset dystonia, and liver cirrhosis (HMDPC). To-date only 14 families from various ethnic groups have been reported. Here, we describe 10 patients from 7 unrelated Egyptian families with HMDPC. Markedly elevated blood Mn levels, the characteristic basal ganglia hyperintensity on T1W images, and variable degrees of extrapyramidal manifestations with or without liver disease were cardinal features in all patients...
November 28, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29178603/targeted-next-generation-sequencing-and-parental-genotyping-in-sporadic-chinese-han-deaf-patients
#9
L He, X Pang, H Liu, Y Chai, H Wu, T Yang
The interpretation of the targeted next-generation sequencing (NGS) results can be challenging for variants identified in the sporadic deaf patients. In this study, we performed targeted NGS of 143 deafness-associated genes in 44 sporadic deaf patients and use parental genotyping to test whether the candidate pathogenic variants complied with recessive or de novo pattern. Of 29 recessive candidate variants with minor allele frequencies less than 0.005, three pairs of apparent compound heterozygous variants were inherited from the same parental allele, ruling out their pathogenic roles...
November 27, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29178422/novel-inactivating-mutations-of-the-dcaf17-gene-in-american-and-turkish-families-cause-male-infertility-and-female-subfertility-in-the-mouse-model
#10
F Gurbuz, S Desai, F Diao, F Wranitz, M Wood-Trageser, Y-H Shin, L Damla Kotan, H Jiang, S Witchel, N Gurtunca, S Yatsenko, D Mysliwec, K Topaloglu, A Rajkovic
Loss of function DCAF17 variants cause hypogonadism, partial alopecia, diabetes mellitus, mental retardation, and deafness with variable clinical presentation ranging. DCAF17 pathogenic variants have been largely reported in the Middle Eastern populations, but the incidence in American families is rare and animal models are lacking. Exome sequencing in five women with syndromic hypergonadotropic hypogonadism from two unrelated families revealed novel pathogenic variants in the DCAF17 gene. DCAF17 exon 2 (c...
November 27, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29178324/effect-of-lsr-polymorphism-on-blood-lipid-levels-and-age-specific-epistatic-interaction-with-the-apoe-common-polymorphism
#11
T Xie, M G Stathopoulou, S Akbar, T Oster, G Siest, F T Yen, S Visvikis-Siest
The lipolysis stimulated lipoprotein receptor (LSR) is an apolipoprotein (Apo) B and ApoE receptor that participates in the removal of TG-rich lipoproteins during the postprandial phase. LSR gene is located upstream of APOE, an important risk factor for cardiovascular disease (CVD). Since the APOE common polymorphism significantly affects the variability of lipid metabolism, this study aimed to determine the potential impact of a functional SNP rs916147 in LSR gene on lipid traits in healthy subjects and to investigate potential epistatic interaction between LSR and APOE...
November 27, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29136284/patient-outcomes-of-genetic-counseling-assessing-the-impact-of-different-approaches-to-family-history-collection
#12
C Slomp, E Morris, A Inglis, A Lehman, J Austin
No studies have evaluated whether different modalities for collection of family history data influence patient outcomes of genetic counseling. We retrospectively compared outcomes of genetic counseling between patients whose family history (Fhx) was collected: a) via telephone prior to their appointment (FhxPrior), or b) during the appointment (FhxDuring). We used a psychiatric genetic counseling clinic database, where information about demographics and Fhx timing is recorded and patients complete the Genetic Counseling Outcomes Scale (GCOS, measuring empowerment) and Illness Management Self-Efficacy Scale (IMSES) immediately prior to (T1) and one-month after their appointment (T2)...
November 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29136281/genetic-prediction-of-type-2-diabetes-using-deep-neural-network
#13
J Kim, J Kim, M J Kwak, M Bajaj
Type 2 diabetes (T2DM) has strong heritability but genetic models to explain heritability have been challenging. We tested deep neural network (DNN) to predict T2DM using the nested case-control study of Nurses' Health Study (3,326 females, 45.6% T2DM) and Health Professionals Follow-up Study (2,502 males, 46.5% T2DM). We selected 96, 214, 399, and 678 SNPs through Fisher's exact test and L1-penalized logistic regression. We split each dataset randomly in 4:1 to train prediction models and test their performance...
November 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29136278/a-critical-appraisal-of-pharmacogenetic-inference
#14
REVIEW
R A J Smit, R Noordam, S le Cessie, S Trompet, J W Jukema
In essence, pharmacogenetic research is aimed at discovering variants of importance to gene-treatment interaction. However, epidemiological studies are rarely set up with this goal in mind. It is therefore of great importance that researchers clearly communicate which assumptions they have had to make, and which inherent limitations apply to the interpretation of their results. This review discusses considerations of, and the underlying assumptions for, utilizing different response phenotypes and study designs popular in pharmacogenetic research to infer gene-treatment interaction effects, with a special focus on those dealing with of clinical effects of drug treatment...
November 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29136277/homozygous-xylt2-variants-as-a-cause-of-spondyloocular-syndrome
#15
M Umair, G Eckstein, G Rudolph, T Strom, E Graf, D Hendig, J Hoover, J Alanay, T Meitinger, H Schmidt, W Ahmad
Spondyloocular syndrome (SOS) is a rare autosomal recessive skeletal disorder. Two recent studies have shown that it is the result of biallelic sequence variants in the XYLT2 gene with pleiotropic effects in multiple organs including retina, heart muscle, inner ear, cartilage, and bone. The XYLT2 gene encodes xylosyltransferase 2, which catalyzes the transfer of xylose (monosaccharide) to the core protein of proteoglycans (PG) leading to initiating the process of proteoglycan assembly. SOS was originally characterized in two families A and B of Iraqi and Turkish origin, respectively...
November 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29136273/foxe3-mutations-genotype-phenotype-correlations
#16
J Plaisancié, N K Ragge, H Dollfus, J Kaplan, D Lehalle, C Francannet, G Morin, H Colineaux, P Calvas, N Chassaing
Microphthalmia and anophthalmia (MA) are severe developmental eye anomalies, many of which are likely to have an underlying genetic cause. More than 30 genes have been described, each of which is responsible for a small percentage of these anomalies. Amongst these, is the FOXE3 gene, which was initially described in individuals with dominantly inherited anterior segment dysgenesis and, subsequently, associated with recessively inherited primary aphakia, sclerocornea and microphthalmia. In this work, we describe 8 individuals presenting with a MA phenotype...
November 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29124743/a-novel-germline-mutation-in-cdk4-codon-24-associated-to-familial-melanoma
#17
LETTER
I Bottillo, R La Starza, F C Radio, C Molica, L Pedace, T Pierini, C De Bernardo, L Stingeni, S Bargiacchi, A Paiardini, G Janson, C Mecucci, P Grammatico
No abstract text is available yet for this article.
November 10, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29120068/diagnosis-and-genetics-of-alacrima
#18
REVIEW
J Adams, C P Schaaf
Alacrima, the lack of tears, is a rare clinical finding that has been reported as a feature of multiple genetic disorders and can serve as a diagnostic clue to some rare conditions. Causes of alacrima range from absence/hyposecretion of tears to agenesis or improper development of lacrimal gland ducts and associated structures. There are 13 known heritable disorders featuring varying degrees and causes of alacrima. Some manifest only the congenital absence of tears, while others affect multiple organ systems and may involve severe developmental delay, intellectual disability, and potentially life-threatening autonomic dysregulation...
November 9, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29120067/review-of-patient-decision-making-factors-and-attitudes-regarding-preimplantation-genetic-diagnosis
#19
REVIEW
Margaux C Genoff Garzon, Lisa R Rubin, Marci Lobel, James Stelling, Lisa M Pastore
The increasing technical complexity and evolving options for repro-genetic testing have direct implications for information processing and decision-making, yet the research among patients considering preimplantation genetic diagnosis (PGD) is narrowly focused. This review synthesizes the literature regarding patient PGD decision-making factors, and illuminates gaps for future research and clinical translation. Twenty-five articles met the inclusion criteria for evaluating experiences and attitudes of patients directly involved in PGD as an intervention or considering using PGD...
November 9, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29120066/a-novel-nonsense-variant-in-reep6-is-involved-in-a-sporadic-rod-cone-dystrophy-case
#20
C Méjécase, S Mohand-Saïd, S El Shamieh, A Antonio, C Condroyer, S Blanchard, M Letexier, J-P Saraiva, J-A Sahel, I Audo, C Zeitz
Rod-cone dystrophy (RCD), also called retinitis pigmentosa, is the most common form of progressive inherited retinal disorders secondary to photoreceptor degeneration. It is a genetically heterogeneous disease characterized by night blindness, followed by visual field constriction and, in most severe cases, total blindness. The aim of our study was to identify the underlying gene defect leading to severe RCD in a 60-year-old woman. The patient's DNA was investigated by targeted next generation sequencing followed by whole exome sequencing...
November 9, 2017: Clinical Genetics
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