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https://www.readbyqxmd.com/read/28345382/identification-of-a-novel-nonsense-mutation-of-the-neurotrophic-tyrosine-kinase-receptor-type-1-gene-in-two-siblings-with-congenital-insensitivity-to-pain-with-anhidrosis
#1
Ting Wang, Haibo Li, Jingjing Xiang, Bin Wei, Qin Zhang, Qin Zhu, Minjuan Liu, Miao Sun, Hong Li
Objective To explore the aetiology of congenital insensitivity to pain with anhidrosis (CIPA) in two Chinese siblings with typical CIPA symptoms including insensitivity to pain, inability to sweat, and self-mutilating behaviours. Methods Clinical examination and genetic testing were conducted of all available family members, and the findings were used to create a pedigree. Mutation screening using PCR amplification and DNA Sanger sequencing of the entire neurotrophic tyrosine kinase receptor type 1 gene ( NTRK1) including intron-exon boundaries was used to identify mutations associated with CIPA...
January 1, 2017: Journal of International Medical Research
https://www.readbyqxmd.com/read/28342368/set-up-of-cutoff-thresholds-for-kinship-determination-using-snp-loci
#2
Sohee Cho, Eun Soon Shin, Hyung Jin Yu, Ji Hyun Lee, Hee Jin Seo, Moon Young Kim, Soong Deok Lee
The usefulness of single nucleotide polymorphism (SNP) loci for kinship testing has been demonstrated in many case works, and suggested as a promising marker for relationship identification. For interpreting results based on the calculation of the likelihood ratio (LR) in kinship testing, it is important to prepare cutoffs for respective relatives which are dependent on genetic relatedness. For this, analysis using true pedigree data is significant and reliable as it reflects the actual frequencies of markers in the population...
March 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28341647/estimating-seven-coefficients-of-pairwise-relatedness-using-population-genomic-data
#3
Matthew S Ackerman, Parul Johri, Ken Spitze, Sen Xu, Thomas G Doak, Kimberly Young, Michael Lynch
Population structure can be described by genotypic correlation coefficients between groups of individuals, the most basic of which are the pair-wise relatedness coefficients between any two individuals. There are nine pair-wise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci. Although all nine coefficients can be estimated from pedigrees, six coefficients have been beyond empirical reach. We provide a numerical optimization procedure that estimates all seven reduced coefficients from population-genomic data...
March 24, 2017: Genetics
https://www.readbyqxmd.com/read/28341209/a-non-zero-variance-of-tajima-s-estimator-for-two-sequences-even-for-infinitely-many-unlinked-loci
#4
Léandra King, John Wakeley, Shai Carmi
The population-scaled mutation rate, θ, is informative on the effective population size and is thus widely used in population genetics. We show that for two sequences and n unlinked loci, the variance of Tajima's estimator (θˆ), which is the average number of pairwise differences, does not vanish even as n→∞. The non-zero variance of θˆ results from a (weak) correlation between coalescence times even at unlinked loci, which, in turn, is due to the underlying fixed pedigree shared by gene genealogies at all loci...
March 21, 2017: Theoretical Population Biology
https://www.readbyqxmd.com/read/28341050/development-of-genetic-and-genomic-evaluation-for-wellness-traits-in-us-holstein-cows
#5
N Vukasinovic, N Bacciu, C A Przybyla, P Boddhireddy, S K DeNise
In March 2016, Zoetis Genetics offered the first commercially available evaluation for wellness traits of Holstein dairy cattle. Phenotypic data on health events, pedigree, and genotypes were collected directly from producers upon obtaining their permission. Among all recorded health events, 6 traits were chosen to be included in the evaluation: mastitis, metritis, retained placenta, displaced abomasum, ketosis, and lameness. Each trait was defined as a binary event, having a value of 1 if a cow has been recorded with a disorder at any point during the lactation and zero otherwise...
January 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28341049/accuracy-of-breeding-values-in-small-genotyped-populations-using-different-sources-of-external-information-a-simulation-study
#6
S Andonov, D A L Lourenco, B O Fragomeni, Y Masuda, I Pocrnic, S Tsuruta, I Misztal
Genetically linked small and large dairy cattle populations were simulated to test the effect of different sources of information from foreign populations on the accuracy of predicting breeding values for young animals in a small population. A large dairy cattle population (PL) with >20 generations was simulated, and a small subpopulation (PS) with 3 generations was formed as a related population, including phenotypes and genomic information. Predicted breeding values for young animals in the small population were calculated using BLUP and single-step genomic BLUP (ssGBLUP) in 4 different scenarios: (S1) 3,166 phenotypes, 22,855 pedigree animals, and 1,000 to 6,000 genotypes for PS; (S2) S1 plus genomic estimated breeding value (GEBV) for 4,475 sires from PL as external information; (S3) S1 plus 221,580 phenotypes, 402,829 pedigree animals, and 53,558 genotypes for PL; and (S4) single nucleotide polymorphism (SNP) effects calculated based on PL data...
January 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28340953/clinical-features-of-chinese-patients-with-gerstmann-str%C3%A3-ussler-scheinker-identified-by-targeted-next-generation-sequencing
#7
Hong-Fu Li, Zhi-Jun Liu, Hai-Lin Dong, Juan-Juan Xie, Shao-Yun Zhao, Wang Ni, Yi Dong, Zhi-Ying Wu
Gerstmann-Sträussler-Scheinker (GSS) is an autosomal dominant neurodegenerative disease due to mutations within prion protein (PRNP) gene. Clinically, it is not easy to distinguish GSS from spinocerebellar ataxia (SCA), especially in the early stage of disease. We aimed to identify genetic mutations in 8 Chinese pedigrees with dominant ataxia but excluded dynamic mutations of SCA genes. Targeted next-generation sequencing was performed in the 8 probands. A customized panel was designed to capture 24 known causative genes, including 15 autosomal dominant SCA genes and 9 dementia-related genes...
January 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28339774/genetic-basis-of-leg-health-and-its-relationship-with-body-weight-in-purebred-turkey-lines
#8
D N R G Kapell, P M Hocking, P K Glover, V D Kremer, S Avendaño
The aims of this study were to estimate the genetic parameters for leg and foot health and mobility in purebred turkey lines and their genetic correlations with BW. Traits were gait score (GS) as an overall measure of leg health, footpad dermatitis (FPD), and 2 skeletal leg health traits, namely, valgus and varus deformities (VVD) and tibial dyschondroplasia (TD). Data from 4 different lines, comprising 3 yr of phenotypic records and 4 yr of pedigree information per line, were used. The sex average BW for the lines at 18 wk ranged from 19...
February 23, 2017: Poultry Science
https://www.readbyqxmd.com/read/28338805/deciphering-the-genetic-control-of-fruit-texture-in-apple-by-multiple-family-based-analysis-and-genome-wide-association
#9
Mario Di Guardo, Marco C A M Bink, Walter Guerra, Thomas Letschka, Lidia Lozano, Nicola Busatto, Lara Poles, Alice Tadiello, Luca Bianco, Richard G F Visser, Eric van de Weg, Fabrizio Costa
Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions...
February 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338098/genome-wide-random-regression-analysis-for-parent-of-origin-effects-of-body-composition-allometries-in-mouse
#10
Jingli Zhao, Shuling Li, Lijuan Wang, Li Jiang, Runqing Yang, Yuehua Cui
Genomic imprinting underlying growth and development traits has been recognized, with a focus on the form of absolute or pure growth. However, little is known about the effect of genomic imprinting on relative growth. In this study, we proposed a random regression model to estimate genome-wide imprinting effects on the relative growth of multiple tissues and organs to body weight in mice. Joint static allometry scaling equation as sub-model is nested within the genetic effects of markers and polygenic effects caused by a pedigree...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28335728/allelic-incompatibility-can-explain-female-biased-sex-ratios-in-dioecious-plants
#11
Pascal Pucholt, Henrik R Hallingbäck, Sofia Berlin
BACKGROUND: Biased sex ratios are common among dioecious plant species despite the theoretical prediction of selective advantage of even sex ratios. Albeit the high prevalence of deviations from even sex ratios, the genetic causes to sex biases are rarely known outside of a few model species. Here we present a mechanism underlying the female biased sex ratio in the dioecious willow species Salix viminalis. RESULTS: We compared the segregation pattern of genome-wide single nucleotide polymorphism markers in two contrasting bi-parental pedigree populations, the S3 with even sex ratio and the S5 with a female biased sex ratio...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28331626/osteosarcoma-inheritance-in-two-families-of-scottish-deerhounds
#12
John E Dillberger, Sara Ann McAtee
BACKGROUND: Osteosarcoma is the most common neoplastic disease in Scottish Deerhounds. For Deerhounds, a 2007 population-based study concluded that a single dominant genetic factor largely governed disease risk. For Greyhounds, Rottweilers, and Irish Wolfhounds, a 2013 genome-wide association study found multiple genetic markers in each breed, with each marker only weakly associated with the disease. We obtained from two breeders the pedigrees, age (if alive) or age at death, and osteosarcoma status for two families of Scottish Deerhounds, designated Cohorts K and T...
2017: Canine Genetics and Epidemiology
https://www.readbyqxmd.com/read/28331200/pedigree-based-genome-re-sequencing-reveals-genetic-variation-patterns-of-elite-backbone-varieties-during-modern-rice-improvement
#13
Xingfei Zheng, Lanzhi Li, Fan Liang, Changjun Tan, Shuzhu Tang, Sibin Yu, Ying Diao, Shuangcheng Li, Zhongli Hu
Rice breeding has achieved great productivity improvements by semi-dwarf varieties and hybrid vigour. Due to poor understanding of genetic basis of elite backbone varieties, the continuous increasing in rice yield still faces great challenges. Here, 52 elite rice varieties from three historical representative pedigrees were re-sequenced with 10.1× depth on average, and ~6.5 million single nucleotide polymorphisms (SNPs) were obtained. We identified thousands of low-diversity genomic regions and 0-diversity genes during breeding...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28330290/successful-cloning-of-an-adult-breeding-boar-from-the-novel-chinese-guike-no-1-swine-specialized-strain
#14
Jun-Yu Nie, Xiang-Xing Zhu, Bing-Kun Xie, Su-Qun Nong, Qing-Yan Ma, Hui-Yan Xu, Xiao-Gan Yang, Yang-Qing Lu, Ke-Huan Lu, Yu-Ying Liao, Sheng-Sheng Lu
Somatic cloning, also known as somatic cell nuclear transfer (SCNT), is a promising technology which has been expected to rapidly extend the population of elaborately selected breeding boars with superior production performance. Chinese Guike No. 1 pig breed is a novel swine specialized strain incorporated with the pedigree background of Duroc and Chinese Luchuan pig breeds, thus inherits an excellent production performance. The present study was conducted to establish somatic cloning procedures of adult breeding boars from the Chinese Guike No...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328508/hapiso-an-accurate-method-for-the-haplotype-specific-isoforms-reconstruction-from-long-single-molecule-reads
#15
Serghei Mangul, Harry Taegyun Yang, Farhad Hormozdiari, Alex Dainis, Elizabeth Tseng, Euan A Ashley, Alex Zelikovsky, Eleazar Eskin
Sequencing of RNA provides the possibility to study an individual's transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms...
March 17, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28326674/whole-exome-sequencing-with-genomic-triangulation-implicates-cdh2-encoded-n-cadherin-as-a-novel-pathogenic-substrate-for-arrhythmogenic-cardiomyopathy
#16
Kari L Turkowski, David J Tester, J Martijn Bos, Kristina H Haugaa, Michael J Ackerman
BACKGROUND: Arrhythmogenic cardiomyopathy (ACM) is a heritable disease characterized by fibrofatty replacement of cardiomyocytes, has a prevalence of approximately 1 in 5000 individuals, and accounts for approximately 20% of sudden cardiac death in the young (≤35 years). ACM is most often inherited as an autosomal dominant trait with incomplete penetrance and variable expression. While mutations in several genes that encode key desmosomal proteins underlie about half of all ACM, the remainder is elusive genetically...
March 21, 2017: Congenital Heart Disease
https://www.readbyqxmd.com/read/28324246/opinions-of-hearing-parents-about-the-causes-of-hearing-impairment-of-their-children-with-biallelic-gjb2-mutations
#17
Aisen V Solovyev, Lilya U Dzhemileva, Olga L Posukh, Nikolay A Barashkov, Marita S Bady-Khoo, Semen L Lobov, Natalya Yu Popova, Georgii P Romanov, Nikolay N Sazonov, Alexander A Bondar, Igor V Morozov, Mikhail I Tomsky, Sardana A Fedorova, Elza K Khusnutdinova
Hereditary hearing impairment (HI) caused by recessive GJB2 mutations is a frequent sensory disorder. The results of the molecular-based studies of HI are widely used in various genetic test systems. However, the ethical aspects are less described than the genetic aspects. The concerns expressed by individuals from groups with genetic risks must be included in the counseling of patients and their families. For evaluation of subjective opinions of hearing parents about the presumed causes of HI of their children, we analyze the cohort of parents having children with confirmed hereditary HI caused by biallelic recessive GJB2 mutations (in a homozygous or a compound heterozygous state)...
March 21, 2017: Journal of Community Genetics
https://www.readbyqxmd.com/read/28324054/ccdc141-mutations-in-idiopathic-hypogonadotropic-hypogonadism
#18
Ihsan Turan, B Ian Hutchins, Bulent Hacihamdioglu, L Damla Kotan, Fatih Gurbuz, Ayca Ulubay, Eda Mengen, Bilgin Yuksel, Susan Wray, A Kemal Topaloglu
Context: GnRH neurons originate outside the central nervous system in the olfactory placode and migrate into the CNS, becoming integral components of the hypothalamic-pituitary-gonadal axis. Failure of this migration can lead to Idiopathic Hypogonadotropic Hypogonadism (IHH)/Kallmann Syndrome (KS). We have previously shown that CCDC141 knockdown leads to impaired migration of GnRH neurons but not of olfactory receptor neurons. Objective: The aim of this study was to further describe the phenotype and prevalence of CCDC141 mutations in IHH/KS...
January 23, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28322501/multigenerational-pedigree-with-star-syndrome-a-novel-fam58a-variant-and-expansion-of-the-phenotype
#19
Nicole J Boczek, Teresa Kruisselbrink, Margot A Cousin, Patrick R Blackburn, Eric W Klee, Ralitza H Gavrilova, Brendan C Lanpher
STAR syndrome is a rare X-linked dominant disorder characterized by toe Syndactyly, Telecanthus, Anogenital malformations, and Renal malformations, and is caused by loss-of-function variants in FAM58A. Our proband presented with the hallmark features of STAR syndrome, as well as some additional less typical features including tethered cord and hearing loss. The proband's mother and maternal half-sister had similar clinical histories, but had variability in phenotypic severity. Clinical whole exome sequencing revealed a novel pathogenic nonsense variant, c...
March 21, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28322220/early-onset-progressive-retinal-atrophy-associated-with-an-iqcb1-variant-in-african-black-footed-cats-felis-nigripes
#20
Annie Oh, Jacqueline W Pearce, Barbara Gandolfi, Erica K Creighton, William K Suedmeyer, Michael Selig, Ann P Bosiack, Leilani J Castaner, Rebecca E H Whiting, Ellen B Belknap, Leslie A Lyons
African black-footed cats (Felis nigripes) are endangered wild felids. One male and full-sibling female African black-footed cat developed vision deficits and mydriasis as early as 3 months of age. The diagnosis of early-onset progressive retinal atrophy (PRA) was supported by reduced direct and consensual pupillary light reflexes, phenotypic presence of retinal degeneration, and a non-recordable electroretinogram with negligible amplitudes in both eyes. Whole genome sequencing, conducted on two unaffected parents and one affected offspring was compared to a variant database from 51 domestic cats and a Pallas cat, revealed 50 candidate variants that segregated concordantly with the PRA phenotype...
March 21, 2017: Scientific Reports
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