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Jeffrey B Endelman, Cari A Schmitz Carley, Paul C Bethke, Joseph J Coombs, Mark E Clough, Washington L da Silva, Walter S De Jong, David S Douches, Curtis M Frederick, Kathleen G Haynes, David G Holm, J Creighton Miller, Patricio R Muñoz, Felix M Navarro, Richard G Novy, Jiwan P Palta, Gregory A Porter, Kyle T Rak, Vidyasagar R Sathuvalli, Asunta L Thompson, G Craig Yencho
As one of the world's most important food crops, potato ( Solanum tuberosum L.) has spurred innovation in autotetraploid genetics, including the use of SNP arrays to determine allele dosage at thousands of markers. By combining genotype and pedigree information with phenotype data for economically important traits, the objectives of this study were to (1) partition the genetic variance into additive vs. non-additive components, and (2) determine the accuracy of genome-wide prediction. Between 2012 and 2017, a training population of 571 clones was evaluated for total yield, specific gravity, and chip fry color...
March 7, 2018: Genetics
C M Mak, S Pl Chen, N S Mok, W K Siu, H Hc Lee, C K Ching, P T Tsui, N C Fong, Y P Yuen, W T Poon, C Y Law, Y K Chong, Y W Chan, T C Yung, K Yy Fan, C W Lam
INTRODUCTION: Hereditary channelopathies and cardiomyopathies are potentially lethal and are clinically and genetically heterogeneous, involving at least 90 genes. Genetic testing can provide an accurate diagnosis, guide treatment, and enable cascade screening. The genetic basis among the Hong Kong Chinese population is largely unknown. We aimed to report on 28 unrelated patients with positive genetic findings detected from January 2006 to December 2015. METHODS: Sanger sequencing was performed for 28 unrelated patients with a clinical diagnosis of channelopathies or cardiomyopathies, testing for the following genes: KCNQ1, KCNH2, KCNE1, KCNE2, and SCN5A, for long QT syndrome; SCN5A for Brugada syndrome; RYR2 for catecholaminergic polymorphic ventricular tachycardia; MYH7 and MYBPC3 for hypertrophic cardiomyopathy; LMNA for dilated cardiomyopathy; and PKP2 and DSP for arrhythmogenic right ventricular dysplasia/cardiomyopathy...
March 2, 2018: Hong Kong Medical Journal, Xianggang Yi Xue za Zhi
Clara Sm Tang, Xuehan Zhuang, Wai-Yee Lam, Elly Sau-Wai Ngan, Jacob Shujui Hsu, Y U Michelle, S O Man-Ting, Stacey S Cherny, Ngoc Diem Ngo, Pak C Sham, Paul Kh Tam, Maria-Mercè Garcia-Barcelo
Hirschsprung disease (HSCR) is a complex birth defect characterized by the lack of ganglion cells along a variable length of the distal intestine. A large proportion of HSCR patients remain genetically unexplained. We applied whole-genome sequencing (WGS) on 9 trios where the probands are sporadically affected with the most severe form of the disorder and harbor no coding sequence variants affecting the function of known HSCR genes. We found de novo protein-altering variants in three intolerant to change genes-CCT2, VASH1, and CYP26A1-for which a plausible link with the enteric nervous system (ENS) exists...
February 26, 2018: European Journal of Human Genetics: EJHG
Kenneth E McCarson, Michelle K Winter, Dale R Abrahamson, Nancy E Berman, Peter G Smith
Behavioral phenotyping is a crucial step in validating animal models of human disease. Most traditional behavioral analyses rely on investigator observation of animal subjects, which can be confounded by inter-observer variability, scoring consistency, and the ability to observe extremely rapid, small, or repetitive movements. Force-Plate Actimeter (FPA)-based assessments can quantify locomotor activity and detailed motor activity with an incredibly rich data stream that can reveal details of movement unobservable by the naked eye...
February 21, 2018: Neurobiology of Learning and Memory
Naeela Qureshi, Harbans Bariana, Vikas Venu Kumran, Sivasamy Muruga, Kerrie L Forrest, Mathew J Hayden, Urmil Bansal
A new leaf rust resistance gene Lr79 has been mapped in the long arm of chromosome 3B and a linked marker was identified for marker-assisted selection. Aus26582, a durum wheat landrace from the A. E. Watkins Collection, showed seedling resistance against durum-specific and common wheat-specific Puccinia triticina (Pt) pathotypes. Genetic analysis using a recombinant inbred line (RIL) population developed from a cross between Aus26582 and the susceptible parent Bansi with Australian Pt pathotype showed digenic inheritance and the underlying loci were temporarily named LrAW2 and LrAW3...
February 2, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Emilie Cornec-Le Gall, Fouad T Chebib, Charles D Madsen, Sarah R Senum, Christina M Heyer, Brendan C Lanpher, Marc C Patterson, Robert C Albright, Alan S Yu, Vicente E Torres, Peter C Harris
The diagnosis of autosomal dominant polycystic kidney disease (ADPKD) relies on imaging criteria in the setting of a positive familial history. Molecular analysis, seldom used in clinical practice, identifies a causative mutation in >90% of cases in the genes PKD1, PKD2, or rarely GANAB. We report the clinical and genetic dissection of a 7-generation pedigree, resulting in the diagnosis of 2 different cystic disorders. Using targeted next-generation sequencing of 65 candidate genes in a patient with an ADPKD-like phenotype who lacked the familial PKD2 mutation, we identified a COL4A1 mutation (p...
January 27, 2018: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
Nik Nairan Abdullah, Suzanna Daud, Seok Mui Wang, Zamalia Mahmud, Noor Kaslina Mohd Kornain, Waqar Al-Kubaisy
This study aims to determine the acceptability of Human Papilloma Virus (HPV) self-sampling and the factors associated with willingness to buy HPV self-sampling kit in the future. A total of 164 women aged 28-60 years old from Obstetrics & Gynaecology clinics at a teaching hospital performed HPV self-sampling using the Digene HC2 DNA collection kit. After samples were taken, the participants were given self-administered questionnaires. The majority of the participants were Malay (93.9%), had attained tertiary education (65...
January 31, 2018: Journal of Obstetrics and Gynaecology: the Journal of the Institute of Obstetrics and Gynaecology
Marzieh Naseri, Masoud Akbarzadehlaleh, Marjan Masoudi, Najmeh Ahangari, Ali Akbar Poursadegh Zonouzi, Ahmad Poursadegh Zonouzi, Leila Shams, Azim Nejatizadeh
Background: Autosomal recessive non-syndromic hearing loss (ARNSHL) a most frequent hereditary type of hearing impairment, exhibit tremendous genetic heterogeneity. We aimed to determine the contribution of three common DFNB loci (DFNB4, DFNB28, and DFNB93), and mutation analysis of Gap Junction Beta-2 gene (GJB2) and GJB3 genes in ARNSHL subjects in southern Iran. Methods: Thirty-six large ARNSHL pedigrees (167 individuals) with at least two affected subjects (72 patients) were included in this descriptive study from Hormozgan Province of Iran, during 2014 - 2015...
January 2018: Iranian Journal of Public Health
Toshiyuki Sasagawa, Toshiyuki Maehama, Yasuhiro Osaka, Jinichi Sakamoto, Takeo Shibata, Satoko Fujita, Masahiro Takakura, Hiroaki Takagi
To examine validity of the hybrid capture-2 and cobas 4800 HPV tests, 396 women including 188 women visiting for cancer screening, and 208 referral cases were examined with both HPV tests and the liquid-based cervical Pap test. Concordant results between the HPV assays were observed in 333 cases (coincident rates; 84.1%, kappa value; 0.682). The sensitivity for CIN2+ was 98.6% (69/70) and 82.9% (58/70) for HC2 and cobas 4800 (McNemar's test; P = 0.0026). The sensitivity for CIN3+ was 97.2% (35/36) and 83...
January 5, 2018: Journal of Medical Virology
Kaitian Chen, Yuan Zhan, Xuan Wu, Ling Zong, Hongyan Jiang
OBJECTIVES: Waardenburg syndrome mutations are most often recurrent or de novo. The rate of familial recurrence is low and families with several affected children are extremely rare. In this study, we aimed to clarify the underlying hereditary cause of Waardenburg syndrome type I in two siblings in a Chinese family, with a mother affected by prelingual mild hearing loss and a father who was negative for clinical symptoms of Waardenburg syndrome and had a normal hearing threshold. METHODS: Complete characteristic features of the family members were recorded and genetic sequencing and parent-child relationship analyses were performed...
January 2018: International Journal of Pediatric Otorhinolaryngology
Yuanfeng Gao, Chongyou Lee, Junxian Song, Sufang Li, Yuxia Cui, Yongzhen Liu, Jie Wang, Fengmin Lu, Hong Chen
Genetic factors play a vital role in the pathogenesis of premature myocardial infarction (PMI). However, current studies explained only small amounts of genetic risk in MI. In this study, we started from a PMI pedigree with three MI patients occurred at the age of 43, 45 and 53 respectively. Sanger sequencing revealed 6 LDLR mutation carriers in the family, but only one was diagnosed with PMI, indicating that the LDLR mutation may not be the reason for PMI. Upon exome-sequencing and bioinformatics analysis, two variants in SCAP and AGXT2 were identified as potential causative mutation for PMI...
November 21, 2017: Oncotarget
Xueli Zhang, Congwei Sun, Zheng Zhang, Zhijun Dai, Yuan Chen, Xiong Yuan, Zheming Yuan, Wenbang Tang, Lanzhi Li, Zhongli Hu
The use of heterosis has considerably increased the productivity of many crops; however, the biological mechanism underpinning the technique remains elusive. The North Carolina design III (NCIII) and the triple test cross (TTC) are powerful and popular genetic mating design that can be used to decipher the genetic basis of heterosis. However, when using the NCIII design with the present quantitative trait locus (QTL) mapping method, if epistasis exists, the estimated additive or dominant effects are confounded with epistatic effects...
2017: PloS One
Eva König, Claudia Béu Volpato, Benedetta Maria Motta, Hagen Blankenburg, Anne Picard, Peter Pramstaller, Michela Casella, Werner Rauhe, Giulio Pompilio, Viviana Meraviglia, Francisco S Domingues, Elena Sommariva, Alessandra Rossini
BACKGROUND: Arrhythmogenic cardiomyopathy (ACM) is an inherited genetic disorder, characterized by the substitution of heart muscle with fibro-fatty tissue and severe ventricular arrhythmias, often leading to heart failure and sudden cardiac death. ACM is considered a monogenic disorder, but the low penetrance of mutations identified in patients suggests the involvement of additional genetic or environmental factors. METHODS: We used whole exome sequencing to investigate digenic inheritance in two ACM families where previous diagnostic tests have revealed a PKP2 mutation in all affected and some healthy individuals...
December 8, 2017: BMC Medical Genetics
Mehmet Kulhan, Nur G Kulhan, Yasemin Seven, Umit A Nayki, Cenk Nayki, Nahit Ata, Pasa Ulug
Aim of the study: The present study aims to estimate the prevalence and distribution of HPV genotypes and identify related risk factors among Turkish women. Material and methods: 11 624 Turkish women attending our gynaecological clinic and expressing a desire for access to cervical cancer screening were assessed during the years 2014-2016. Cervical specimens were collected and transported using the HC2 HPV DNA Collection Device (consisting of a cervical brush and digene Specimen Transport Medium)...
2017: Contemporary Oncology Współczesna Onkologia
Jenny C McCloskey, W Martin Kast, James P Flexman, Dugald McCallum, Martyn A French, Michael Phillips
BACKGROUND: Anal intraepithelial neoplasia is associated with high-risk human papillomavirus (hrHPV) as a precursor to anal cancer. However, factors other than hrHPV are likely to be involved and further study of cofactors is required because of the possibility of syndemic interactions. METHODS: Three hundred and fourteen patients underwent 457 operations. Histopathology and hrHPV testing using the Digene Hybrid Capture 2 (HC 2) method were performed. Demographic factors and sexually transmissible infections (STIs) were recorded...
December 2017: Papillomavirus Research
Rodrigo Hoyos-Bachiloglu, Janet Chou, Catherine N Sodroski, Abdallah Beano, Wayne Bainter, Magdalena Angelova, Eman Al Idrissi, Murad K Habazi, Hamza Ali Alghamdi, Fahd Almanjomi, Mohamed Al Shehri, Nagi Elsidig, Morsi Alaa Eldin, David M Knipe, Mofareh AlZahrani, Raif S Geha
Primary immunodeficiencies are often monogenic disorders characterized by vulnerability to specific infectious pathogens. Here, we performed whole-exome sequencing of a patient with disseminated Mycobacterium tuberculosis, Streptococcus viridians bacteremia, and cytomegalovirus (CMV) viremia and identified mutations in 2 genes that regulate distinct IFN pathways. The patient had a homozygous frameshift deletion in IFNGR2, which encodes the signal transducing chain of the IFN-γ receptor, that resulted in minimal protein expression and abolished downstream signaling...
November 6, 2017: Journal of Clinical Investigation
Natarajan N Srikrupa, Sundaramurthy Srilekha, Parveen Sen, Tharigopala Arokiasamy, Meenakshi Swaminathan, Muna Bhende, Suman Kapur, Nagasamy Soumittra
The prevalence of mutations in Leber congenital amaurosis (LCA) candidate genes varies in different populations and comprehensive data from a larger Indian cohort on known candidate genes is still unavailable. Ninety-two subjects were recruited after complete ophthalmic examination and informed consent. Targeted re-sequencing of 20 candidate genes was performed using Agilent HaloPlex target enrichment assay and sequenced on Ilumina MiSeq platform. The data was analyzed using standard bioinformatics pipeline, variants annotated, validated and segregated...
October 25, 2017: Clinical Genetics
Majdi Nagara, Gregory Papagregoriou, Rim Ben Abdallah, Zied Landoulsi, Yosra Bouyacoub, Sahar Elouej, Rym Kefi, Tommaso Pippucci, Konstantinos Voskarides, Anu Bashamboo, Kenneth McElreavey, Mongia Hachicha, Giovanni Romeo, Marco Seri, Constantinos Deltas, Sonia Abdelhak
AIM OF THE STUDY: Recent advances in understanding the underlying molecular mechanism for distal renal tubular acidosis (dRTA), led to an increased attention towards the primary and the familial forms of the disease. Mutations in ATP6V1B1 and ATP6V0A4 are usually responsible for the recessive form of the disease. Mutations in gene AE1 encoding the Cl-/HCO3- exchanger, usually present as dominant dRTA, but a recessive pattern has been recently described. Our objective is to identify the mutational spectrum responsible of dRTA in a consanguineous Libyan family...
October 9, 2017: European Journal of Medical Genetics
Athar Khalil, Christiane Al-Haddad, Hadla Hariri, Kamel Shibbani, Fadi Bitar, Mazen Kurban, Georges Nemer, Mariam Arabi
Congenital heart diseases (CHDs) are still the leading cause of death in neonates. Anterior segment dysgenesis is a broad clinical phenotype that affects the normal development of the eye, leading in most of the cases to glaucoma which is still a major cause of blindness for children and adolescents. Despite tremendous insights gained from genetic studies, a clear genotype-phenotype correlation is still difficult to draw. In Lebanon, a small country with still a high rate of consanguineous marriages, there are little data on the epidemiology of glaucoma amongst children with or without CHD...
2017: Frontiers in Cardiovascular Medicine
C Deltas
Digenic inheritance (DI) concerns pathologies with the simplest form of multigenic etiology, implicating more than 1 gene (and perhaps the environment). True DI is when biallelic or even triallelic mutations in 2 distinct genes, in cis or in trans, are necessary and sufficient to cause pathology with a defined diagnosis. In true DI, a heterozygous mutation in each of 2 genes alone is not associated with a recognizable phenotype. Well-documented diseases with true DI are so far rare and follow non-Mendelian inheritance...
March 2018: Clinical Genetics
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