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https://read.qxmd.com/read/30776169/no-evidence-for-an-intragenomic-arms-race-under-paternal-genome-elimination-in-planococcus-mealybugs
#1
Andrés G de la Filia, Gyda Fenn-Moltu, Laura Ross
Genomic conflicts arising during reproduction might play an important role in shaping the striking diversity of reproductive strategies across life. Among these is paternal genome elimination (PGE), a form of haplodiploidy which has independently evolved several times in arthropods. PGE males are diploid but transmit maternally-inherited chromosomes only, while paternal homologues are excluded from sperm. Mothers thereby effectively monopolize the parentage of sons, at the cost of the father's reproductive success...
February 18, 2019: Journal of Evolutionary Biology
https://read.qxmd.com/read/30774704/bayesian-analysis-and-prediction-of-hybrid-performance
#2
Filipe Couto Alves, Ítalo Stefanine Correa Granato, Giovanni Galli, Danilo Hottis Lyra, Roberto Fritsche-Neto, Gustavo de Los Campos
Background: The selection of hybrids is an essential step in maize breeding. However, evaluating a large number of hybrids in field trials can be extremely costly. However, genomic models can be used to predict the expected performance of un-tested genotypes. Bayesian models offer a very flexible framework for hybrid prediction. The Bayesian methodology can be used with parametric and semi-parametric assumptions for additive and non-additive effects. Furthermore, samples from the posterior distribution of Bayesian models can be used to estimate the variance due to general and specific combining abilities even in cases where additive and non-additive effects are not mutually orthogonal...
2019: Plant Methods
https://read.qxmd.com/read/30773532/population-genomic-screening-of-all-young-adults-in-a-health-care-system-a-cost-effectiveness-analysis
#3
Lei Zhang, Yining Bao, Moeen Riaz, Jane Tiller, Danny Liew, Xun Zhuang, David J Amor, Aamira Huq, Lara Petelin, Mark Nelson, Paul A James, Ingrid Winship, John J McNeil, Paul Lacaze
PURPOSE: To consider the impact and cost-effectiveness of offering preventive population genomic screening to all young adults in a single-payer health-care system. METHODS: We modeled screening of 2,688,192 individuals, all adults aged 18-25 years in Australia, for pathogenic variants in BRCA1/BRCA2/MLH1/MSH2 genes, and carrier screening for cystic fibrosis (CF), spinal muscular atrophy (SMA), and fragile X syndrome (FXS), at 71% testing uptake using per-test costs ranging from AUD$200 to $1200 (~USD$140 to $850)...
February 18, 2019: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://read.qxmd.com/read/30769084/considerations-in-multi-gene-panel-testing-in-pediatric-ophthalmology
#4
Amy E Turriff, Catherine Cukras, Brian P Brooks, Laryssa A Huryn
Multi-gene panel testing is used increasingly in ophthalmology practice as an efficient and cost-effective method for diagnosing inherited eye conditions. Panel testing is a powerful diagnostic tool, and it has the potential to reveal syndromic information in patients with seemingly isolated eye findings. This case series highlights our experience with 4 children in 3 families who were referred for evaluation of an isolated retinal degeneration and diagnosed with neuronal ceroid lipofuscinosis on panel testing...
February 12, 2019: Journal of AAPOS: the Official Publication of the American Association for Pediatric Ophthalmology and Strabismus
https://read.qxmd.com/read/30767407/attitude-towards-and-factors-affecting-uptake-of-population-based-brca-testing-in-the-ashkenazi-jewish-population-a-cohort-study
#5
Ranjit Manchanda, Matthew Burnell, Faiza Gaba, Saskia Sanderson, Kelly Loggenberg, Sue Gessler, Jane Wardle, Lucy Side, Rakshit Desai, Angela F Brady, Huw Dorkins, Yvonne Wallis, Cyril Chapman, Chris Jacobs, Ian Tomlinson, Uziel Beller, Usha Menon, Ian Jacobs
OBJECTIVE: To evaluate factors affecting unselected-population-based-BRCA-testing in Ashkenazi-Jews (AJ). DESIGN: Cohort-study set within recruitment to the GCaPPS-trial (ISRCTN73338115). SETTING: North-London AJ-population. POPULATION OR SAMPLE: AJ women/men >18-years, recruited through self-referral. METHODS: AJ-women/men underwent pre-test counselling for BRCA-testing through recruitment clinics (clusters)...
February 15, 2019: BJOG: An International Journal of Obstetrics and Gynaecology
https://read.qxmd.com/read/30766565/single-tube-allele-specific-pcr-a-low-cost-technique-for-molecular-screening-of-sickle-cell-anaemia-in-nigeria
#6
Emuejevoke T Toye, Guido van Marle, Wendy Hutchins, Olayinka Abgabiaje, Joy Okpuzor
Background: Sickle cell anaemia (SCA) is a hereditary blood disorder caused by a single mutation in the haemoglobin gene. The disease burden of SCA is highest in Nigeria. The allele specific polymerase chain reaction (ASPCR) method is applicable for the direct detection of known single nucleotide polymorphisms (SNPs). Objective: To investigate the use of the single tube ASPCR as an accurate and affordable method for SCA screening in Nigeria. Methods: DNA was extracted from study subjects with normal haemoglobin, HbAA (20), sickle cell anaemia, HbSS (20) and carriers, HbAS (1)...
December 2018: African Health Sciences
https://read.qxmd.com/read/30761454/expanded-genetic-carrier-screening-in-clinical-practice-a-current-survey-of-patient-impressions-and-attitudes
#7
Nigel Pereira, Michelle Wood, Emerly Luong, Allison Briggs, Michael Galloway, Rose A Maxwell, Steven R Lindheim
PURPOSE: Expanded genetic carrier screening (ECS) is an important part of gynecological practice and preconception planning. We evaluated the awareness and attitudes among women regarding ECS and factors that may influence decision-making in a family planning context. METHODS: A 32-question survey in an academic university practice was given to 521 women who were either currently pregnant (n = 108), undergoing gynecologic care who were considering future fertility (n = 308), and considering or receiving fertility treatment (n = 105)...
February 13, 2019: Journal of Assisted Reproduction and Genetics
https://read.qxmd.com/read/30759220/a-scalable-aggregated-genotypic-phenotypic-database-for-human-disease-variation
#8
Ryan Barrett, Cynthia L Neben, Anjali D Zimmer, Gilad Mishne, Wendy McKennon, Alicia Y Zhou, Jeremy Ginsberg
Next generation sequencing multi-gene panels have greatly improved the diagnostic yield and cost effectiveness of genetic testing and are rapidly being integrated into the clinic for hereditary cancer risk. With this technology comes a dramatic increase in the volume, type and complexity of data. This invaluable data though is too often buried or inaccessible to researchers, especially to those without strong analytical or programming skills. To effectively share comprehensive, integrated genotypic-phenotypic data, we built Color Data, a publicly available, cloud-based database that supports broad access and data literacy...
January 1, 2019: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/30759195/ensuring-privacy-and-security-of-genomic-data-and-functionalities
#9
Abukari Mohammed Yakubu, Yi-Ping Phoebe Chen
In recent times, the reduced cost of DNA sequencing has resulted in a plethora of genomic data that is being used to advance biomedical research and improve clinical procedures and healthcare delivery. These advances are revolutionizing areas in genome-wide association studies (GWASs), diagnostic testing, personalized medicine and drug discovery. This, however, comes with security and privacy challenges as the human genome is sensitive in nature and uniquely identifies an individual. In this article, we discuss the genome privacy problem and review relevant privacy attacks, classified into identity tracing, attribute disclosure and completion attacks, which have been used to breach the privacy of an individual...
February 12, 2019: Briefings in Bioinformatics
https://read.qxmd.com/read/30747256/the-use-of-fta-cards-to-acquire-dna-profiles-from-postmortem-cases
#10
Henrik Green, Andreas Tillmar, Gisela Pettersson, Kerstin Montelius
Filter papers have been used for many years in different applications of molecular biology and have been proven to be a stable way to store DNA waiting to be analyzed. Sampling of DNA on FTA (Flinders Technology Associates) cards is convenient and cost effective compared to alternative approaches involving DNA extractions and storage of DNA extracts. FTA cards are analyzed at many forensic laboratories, and the way to perform direct genetic profiling on buccal swab cards has developed into an almost industrial process...
February 12, 2019: International Journal of Legal Medicine
https://read.qxmd.com/read/30746499/the-cost-effectiveness-of-multigene-panel-testing-for-hereditary-breast-and-ovarian-cancer-in-norway
#11
Lars Asphaug, Hans Olav Melberg
Background. Expansion of routine genetic testing for hereditary breast and ovarian cancer from conventional BRCA testing to a multigene test could improve diagnostic yield and increase the opportunity for cancer prevention in both identified carriers and their relatives. We use an economic decision model to assess whether the current knowledge on non- BRCA mutation prevalence, cancer risk, and patient preferences justifies switching to a multigene panel for testing of early-onset breast cancer patients. Methods...
January 2019: MDM Policy & Practice
https://read.qxmd.com/read/30739375/is-genomic-diversity-a-useful-proxy-for-census-population-size-evidence-from-a-species-rich-community-of-desert-lizards
#12
Maggie R Grundler, Sonal Singhal, Mark A Cowan, Daniel L Rabosky
Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long-term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome-wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long-term estimates of abundance, occupancy, and degree of ecological specialization in a diverse lizard community from arid Australia...
February 9, 2019: Molecular Ecology
https://read.qxmd.com/read/30736478/emerging-molecular-technologies-in-renal-cell-carcinoma-liquid-biopsy
#13
REVIEW
Alessia Cimadamore, Silvia Gasparrini, Francesco Massari, Matteo Santoni, Liang Cheng, Antonio Lopez-Beltran, Marina Scarpelli, Rodolfo Montironi
Liquid biopsy, based on the circulating tumor cells (CTCs) and cell-free nucleic acids has potential applications at multiple points throughout the natural course of cancer, from diagnosis to follow-up. The advantages of doing ctDNA assessment vs. tissue-based genomic profile are the minimal procedural risk, the possibility to serial testing in order to monitor disease-relapse and response to therapy over time and to reduce hospitalization costs during the entire process. However, some critical issues related to ctDNA assays should be taken into consideration...
February 7, 2019: Cancers
https://read.qxmd.com/read/30735170/determining-the-likelihood-of-variant-pathogenicity-using-amino-acid-level-signal-to-noise-analysis-of-genetic-variation
#14
Edward G Jones, Andrew P Landstrom
Advancements in the cost and speed of next generation genetic sequencing have generated an explosion of clinical whole exome and whole genome testing. While this has led to increased identification of likely pathogenic mutations associated with genetic syndromes, it has also dramatically increased the number of incidentally found genetic variants of unknown significance (VUS). Determining the clinical significance of these variants is a major challenge for both scientists and clinicians. An approach to assist in determining the likelihood of pathogenicity is signal-to-noise analysis at the protein sequence level...
January 16, 2019: Journal of Visualized Experiments: JoVE
https://read.qxmd.com/read/30724335/-small-cost-to-pay-for-peace-of-mind-women-s-experiences-with-non-invasive-prenatal-testing
#15
Hilary Bowman-Smart, Julian Savulescu, Cara Mand, Christopher Gyngell, Mark D Pertile, Sharon Lewis, Martin B Delatycki
BACKGROUND: Non-invasive prenatal testing (NIPT) has been available in Australia on a user-pays basis since 2012. Since its introduction, it has grown in popularity as a screening method for fetal aneuploidy and may become publicly funded. AIMS: To assess the motivations and experiences of women who have undergone NIPT in a user-pays system in Australia. MATERIALS AND METHODS: One thousand women who had undergone NIPT through the Victorian Clinical Genetics Services in Melbourne, Australia were contacted and asked to complete a mixed-methods survey...
February 6, 2019: Australian & New Zealand Journal of Obstetrics & Gynaecology
https://read.qxmd.com/read/30723297/prevalence-of-recurrent-oncogenic-fusion-in-mismatch-repair-deficient-colorectal-carcinoma-with-hypermethylated-mlh1-and-wild-type-braf-and-kras
#16
Jing Wang, Yuting Yi, Yi Xiao, Lin Dong, Li Liang, Lianghong Teng, Jian Ming Ying, Tao Lu, Yuanyuan Liu, Yanfang Guan, Junyi Pang, Lianrui Zhou, Junliang Lu, Zhiwen Zhang, Xiaoding Liu, Xiaolong Liang, Xuan Zeng, Xin Yi, Weixun Zhou, Xuefeng Xia, Ling Yang, Jianjun Zhang, Scott Kopetz, P Andrew Futreal, Huanwen Wu, Zhiyong Liang
Oncogenic fusions are rare in colorectal carcinomas, but may be important for prognosis and therapy. An effective strategy for screening targetable oncogenic fusions in colorectal carcinomas is needed. Here, we investigate molecular genetic alterations in colorectal carcinomas based on their DNA mismatch repair status, and to effectively screen for targetable oncogenic fusions in colorectal carcinomas. In this retrospective study, the initial cohort included 125 consecutive mismatch repair-deficient and 238 randomly selected mismatch repair-proficient colorectal carcinomas diagnosed between July 2015 and December 2017 at Peking Union Medical College Hospital...
February 5, 2019: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://read.qxmd.com/read/30721942/clinical-application-of-embryo-aneuploidy-testing-by-ngs
#17
Carmen Rubio, Lorena Rodrigo, Carmen Garcia-Pascual, Vanessa Peinado, Inmaculada Campos-Galindo, Sandra Garcia-Herrero, Carlos Simón
We review here the evolution in the field of embryo aneuploidy testing over the last 20 years, from the analysis of a subset of chromosomes by fluorescence in situ hybridisation (FISH) to the transition toward a more comprehensive analysis of all 24 chromosomes. This current comprehensive aneuploidy testing most commonly employs next-generation sequencing (NGS). We present our experience in over 130,000 embryo biopsies using this technology. The incidence of aneuploidy was lower in trophectoderm biopsies compared to cleavage-stage biopsies...
February 4, 2019: Biology of Reproduction
https://read.qxmd.com/read/30717118/understanding-implementation-challenges-to-genetic-testing-for-familial-hypercholesterolemia-in-the-united-states
#18
Rachele M Hendricks-Sturrup, Christine Y Lu
Cardiovascular disease (CVD) is the leading cause of death in the United States (US), with familial hypercholesterolemia (FH) being a major inherited and genetic risk factor for premature CVD and atherosclerosis. Genetic testing has helped patients and providers confirm the presence of known pathogenic and likely pathogenic variations in FH-associated genes. Key organizations, such as the Centers for Disease Control and Prevention (CDC), American Heart Association (AHA), FH Foundation, and National Lipid Association (NLA), have recognized the clinical utility of FH genetic testing...
February 1, 2019: Journal of Personalized Medicine
https://read.qxmd.com/read/30710177/distinct-evolutionary-origins-of-common-multi-drug-resistance-phenotypes-in-salmonella-typhimurium-dt104-a-convergent-process-for-adaptation-under-stress
#19
Le Tang, Song-Ling Zhu, Xin Fang, Yong-Guo Li, Cornelis Poppe, Randal N Johnston, Gui-Rong Liu, Shu-Lin Liu
Antimicrobial resistance makes pathogenic bacteria hard to control, but little is known about the general processes of resistance gain or loss. Here, we compared distinct S. typhimurium DT104 strains resistant to zero, two, five, or more of the tested antimicrobials. We found that common resistance phenotypes could be encoded by distinct genes, on SGI-1 or plasmid. We also demonstrated close clonality among all the tested non-resistant and differently resistant DT104 strains, demonstrating dynamic acquisition or loss (by total deletion or gradual decaying of multi-drug resistance gene clusters) of the genetic traits...
February 1, 2019: Molecular Genetics and Genomics: MGG
https://read.qxmd.com/read/30707267/shaping-up-field-deployable-nucleic-acid-testing-using-microfluidic-paper-based-analytical-devices
#20
REVIEW
Tianyu Dong, Guan A Wang, Feng Li
Rapid, low-cost, and sensitive nucleic acid detection and quantification assays enabled by microfluidic paper-based analytical devices (μPADs) hold great promise for point-of-care disease diagnostics and field-based molecular tests. Through the capillary action in μPAD, flexible manipulation of nucleic acid samples can be achieved without the need for external pumps or power supplies, making it possible to fabricate highly integrated sample-to-answer devices that streamline the nucleic acid extraction, separation, concentration, amplification, and detection...
February 1, 2019: Analytical and Bioanalytical Chemistry
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