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1. Consumer genomics will change your life, whether you get tested or not

Author:
Khan, Razib; Mittelman, David
Source:
Genome biology 2018 v.19 no.1 pp. 120
ISSN:
1474-760X
Subject:
genotyping,   etc   ; consumers (people); genomics; industry;     Show all 4 Subjects
Abstract:
... With more than 10 million genotyped customers, the consumer genomics industry is maturing and becoming a mainstream phenomenon. At last, innovations and applications, some unforeseen, are being brought to the masses. ...
DOI:
10.1186/s13059-018-1506-1

2. Performance of 6 HCV genotyping 9G test for HCV genotyping in clinical samples

Author:
Warkad, Shrikant Dasharath; Nimse, Satish Balasaheb; Song, Keum-Soo; Chantratita, Wasun; Pongthanapisith, Viroj; Nawale, Laxman Uddhav; Kim, Taisun
Source:
Virology journal 2018 v.15 no.1 pp. 107
ISSN:
1743-422X
Subject:
genotyping,   etc   ; drugs; hepatitis C; subgenotype;     Show all 4 Subjects
Abstract:
... BACKGROUND: A treatment of HCV infection depends on the genotype and sub-genotype. Therefore, accurate HCV genotyping is critical for selecting the appropriate treatment regimen. METHOD: This study included 280 plasma samples to evaluate the performance of 6 HCV Genotyping 9G test. The performance of 6 HCV Genotyping 9G test for accurate detection of HCV 1a, 1b, 2, 3, 4, and 6 genotypes was evalua ...
DOI:
10.1186/s12985-018-1017-4

3. Detection of an animal-derived G4P[6] group A rotavirus strain in a symptomatic child, in Italy

Author:
Ianiro, Giovanni; Micolano, Roberto; Conte, Michela; Labianca, Michele; Vaccari, Gabriele; Monini, Marina
Source:
Virus research 2019 v.260 pp. 7-11
ISSN:
0168-1702
Subject:
genotyping,   etc   ; Rotavirus A; children; feces; gastroenteritis; genes; genomics; genotype; humans; nucleotide sequences; phylogeny; swine; Asia; Italy;     Show all 14 Subjects
Abstract:
... During 2017, a G4P[6] group A rotavirus strain was identified in the feces of an Italian child hospitalized for acute gastroenteritis in Southern Italy. Nucleotide sequencing of the 11 genomic segments, revealed the G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1 genotype constellation. Phylogenetic analyses of the gene segments investigated revealed high nucleotide sequence identities with G4P[6] RVA strains ...
DOI:
10.1016/j.virusres.2018.11.003

4. A comparison of the MeltPro® HPV Test with the Cobas® HPV Test for detecting and genotyping 14 high-risk human papillomavirus types

Author:
Tang, Zhiteng; Xu, Ye; Song, Najie; Zou, Dongqing; Liao, Yiqun; Li, Qingge; Pan, Chao
Source:
Archives of virology 2018 v.163 no.3 pp. 725-730
ISSN:
0304-8608
Subject:
genotyping,   etc   ; Papillomaviridae; humans; melting curve analysis; monitoring;     Show all 5 Subjects
Abstract:
... The clinical performance of the newly developed MeltPro® HPV Test, based on multicolor melting curve analysis, was evaluated and compared with the commercially available Cobas® HPV Test for detection of HPV and genotyping of HPV-16 and HPV-18. A total of 1647 cervical samples were analyzed with both tests. The agreement values were 96.2% for HPV detection, 99.6% for HPV-16 identification, and 99.7 ...
DOI:
10.1007/s00705-017-3645-1

5. Effects of sampling close relatives on some elementary population genetics analyses

Author:
Wang, Jinliang
Source:
Molecular ecology resources 2018 v.18 no.1 pp. 41-54
ISSN:
1755-098X
Subject:
genotyping,   etc   ; alleles; ecology; gene frequency; heterozygosity; juveniles;     Show all 6 Subjects
Abstract:
... Many molecular ecology analyses assume the genotyped individuals are sampled at random from a population and thus are representative of the population. Realistically, however, a sample may contain excessive close relatives (ECR) because, for example, localized juveniles are drawn from fecund species. Our knowledge is limited about how ECR affect the routinely conducted elementary genetics analyses ...
DOI:
10.1111/1755-0998.12708

6. Genotyping‐by‐sequencing for estimating relatedness in nonmodel organisms: Avoiding the trap of precise bias

Author:
Attard, Catherine R. M.; Beheregaray, Luciano B.; Möller, Luciana M.
Source:
Molecular ecology resources 2018 v.18 no.3 pp. 381-390
ISSN:
1755-098X
Subject:
genotyping by sequencing; genotyping errors,   etc   ; data collection; microsatellite repeats; single nucleotide polymorphism; wildlife;     Show all 6 Subjects
Abstract:
... There has been remarkably little attention to using the high resolution provided by genotyping‐by‐sequencing (i.e., RADseq and similar methods) for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of data that could lead to downward‐biased, yet precise, estimates of relatedness. Here, we assess the applicabi ...
DOI:
10.1111/1755-0998.12739

7. Contribution of α-gliadin alleles to the extensibility of flour dough in Japanese wheat cultivars

Author:
Noma, Satoshi; Hayakawa, Katsuyuki; Abe, Chikako; Suzuki, Sayaka; Kawaura, Kanako
Source:
Journal of cereal science 2019 v.86 pp. 15-21
ISSN:
0733-5210
Subject:
genotyping,   etc   ; Triticum aestivum; alleles; breeding programs; chromosomes; cultivars; dough; dough quality; extensibility; flour; gliadin; seed storage proteins; surveys; wheat;     Show all 14 Subjects
Abstract:
... Alpha-gliadins are one of the major seed storage proteins in wheat and considered involved in wheat dough extensibility. We investigated the relationship between α-gliadin allele types and the extensibility of the resulting flour dough. In a preliminary survey, we identified 26 unique α-gliadin genes expressed in Triticum aestivum L. ‘Chinese Spring’, an experimental standard cultivar. These genes ...
DOI:
10.1016/j.jcs.2018.12.017

8. Paternity analysis using SSR markers reveals that the anthocyanin-rich tea cultivar ‘Ziyan’ is self-compatible

Author:
Tan, Li-Qiang; Liu, Qin-Ling; Zhou, Bin; Yang, Chun-Jing; Zou, Xue; Yu, Ye-Ying; Wang, Yue; Hu, Jin-Hao; Zou, Yao; Chen, Sheng-Xiang; Li, Pin-Wu; Tang, Qian
Source:
Scientia horticulturae 2019 v.245 pp. 258-262
ISSN:
0304-4238
Subject:
genotyping,   etc   ; Camellia sinensis; cultivars; fathers; genetic variation; heterozygosity; inbreeding depression; microsatellite repeats; open pollination; paternity; progeny; seeds; selfing; tea;     Show all 14 Subjects
Abstract:
... Most tea plants (Camellia sinensis) are self-incompatible. Self-incompatibility is critical for preventing inbreeding depression and maintaining genetic diversity, but it can hinder breeding and genetic studies. Originally, the propose of this study was to identify fathers of 16 elite F1 individuals derived from open-pollinated seeds of an anthocyanin-rich tea cultivar ‘Ziyan’. In order to achieve ...
DOI:
10.1016/j.scienta.2018.10.034

9. Human papillomavirus detection in urine: Effect of a first-void urine collection device and timing of collection

Author:
Pattyn, Jade; Van Keer, Severien; Biesmans, Samantha; Ieven, Margareta; Vanderborght, Charlotte; Beyers, Koen; Vankerckhoven, Vanessa; Bruyndonckx, Robin; Van Damme, Pierre; Vorsters, Alex
Source:
Journal of virological methods 2019 v.264 pp. 23-30
ISSN:
0166-0934
Subject:
genotyping,   etc   ; DNA; Papillomaviridae; ambient temperature; biopsy; cohort studies; liquids; quantitative polymerase chain reaction; statistical models; urine; women;     Show all 11 Subjects
Abstract:
... Great interest has been directed towards the use of first-void (FV) urine as a liquid biopsy for high-risk HPV DNA testing. The aim of this study was to investigate the potential effect of a first generation FV urine collection device on the detection of HPV DNA and to assess if the concentration of HPV DNA varies between FV urine collected in the morning and those collected later during the day. ...
DOI:
10.1016/j.jviromet.2018.11.008

10. No apparent fitness costs associated with phytoene desaturase mutations conferred resistance to diflufenican and picolinafen in oriental mustard (Sisymbrium orientale L.)

Author:
Dang, Hue Thi; Long, Weihua; Malone, Jenna Moira; Preston, Christopher; Gill, Gurjeet
Source:
Pesticide biochemistry and physiology 2019
ISSN:
0048-3575
Subject:
genotyping,   etc   ; Sisymbrium orientale; alleles; biomass production; crossing; diflufenican; enzymes; fecundity; point mutation; regression analysis; selection pressure; wheat;     Show all 12 Subjects
Abstract:
... Two mutations Leu498 and Glu425 in the PDS gene were identified as the main cause conferring resistance to diflufenican and picolinafen in two oriental mustard populations P3 and P40. As mutations are suspected to affect fitness, this study was designed to test this hypothesis using the F2 of two crosses P3.2 (P3♂ × S♀) and P40.5 (P40♂ × S♀) of oriental mustard. The F2 plants, which segregated for ...
DOI:
10.1016/j.pestbp.2019.01.005

11. High-throughput blood sample preparation for single nucleotide polymorphism genotyping in less than 25 min

Author:
Wang, Jidong; Zheng, Jiaying; Zhang, Shaohua; Du, Jihui; Chen, Yongxin; Liu, Xiaolei; Zhang, Huisheng; Jiang, Xingyu; Chen, Wenwen
Source:
Talanta 2019 v.191 pp. 119-125
ISSN:
0039-9140
Subject:
genotyping,   etc   ; DNA; blood sampling; blood serum; leukocyte count; protocols; quantitative polymerase chain reaction; single nucleotide polymorphism; triacylglycerols; uric acid;     Show all 10 Subjects
Abstract:
... Straightforward, rapid and high-throughput pretreatment for single nucleotide polymorphisms (SNP) genotyping is critically needed in clinical practice. However, all existing SNP genotyping methods require DNA purification step, which is labor-intensive and time-consuming. We develop a protocol for SNP genotyping by combining whole blood lysis (WBL) with qPCR and justify the practicality of our met ...
DOI:
10.1016/j.talanta.2018.08.051

12. Crop genome‐wide association study: a harvest of biological relevance

Author:
Liu, Hai‐Jun; Yan, Jianbing
Source:
Theplant journal 2019 v.97 no.1 pp. 8-18
ISSN:
0960-7412
Subject:
genotyping,   etc   ; crops; epistasis; gene editing; genome-wide association study; genomics; high-throughput nucleotide sequencing; phenotypic plasticity; pleiotropy;     Show all 9 Subjects
Abstract:
... With the advent of rapid genotyping and next‐generation sequencing technologies, genome‐wide association study (GWAS) has become a routine strategy for decoding genotype–phenotype associations in many species. More than 1000 such studies over the last decade have revealed substantial genotype–phenotype associations in crops and provided unparalleled opportunities to probe functional genomics. Beyo ...
DOI:
10.1111/tpj.14139

13. Mapping kernel texture in a soft durum (Triticum turgidum subsp. durum) wheat population

Author:
Ibba, Maria Itria; Kiszonas, Alecia M.; See, Deven R.; Skinner, Daniel Z.; Morris, Craig F.
Source:
Journal of cereal science 2019 v.85 pp. 20-26
ISSN:
0733-5210
Subject:
genotyping by sequencing,   etc   ; Triticum turgidum subsp. durum; additive effect; alleles; durum wheat; genetic factors; hardness; introgression; loci; seeds; texture;     Show all 11 Subjects
Abstract:
... Kernel texture (”hardness”) is one of the major determinants of wheat quality and is primarily controlled by the Puroindoline (Pin) genes, located at the Hardness (Ha) locus. The absence of the Ha locus is responsible for the extremely hard kernels of durum wheat (T. turgidum subsp. durum). Recently, the Pin genes from a soft common wheat variety were introgressed into durum wheat through homoeolo ...
DOI:
10.1016/j.jcs.2018.10.006

14. A method for the allocation of sequencing resources in genotyped livestock populations

Author:
Gonen, Serap; Ros-Freixedes, Roger; Battagin, Mara; Gorjanc, Gregor; Hickey, JohnM.
Source:
Genetics, selection, evolution 2017 v.49 no.1 pp. 47
ISSN:
1297-9686
Subject:
genotyping,   etc   ; algorithms; haplotypes; livestock; pedigree;     Show all 5 Subjects
Abstract:
... BACKGROUND: This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. METHODS: We present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haploty ...
DOI:
10.1186/s12711-017-0322-5

15. Unambiguous high resolution genotyping of human leukocyte antigens

Author:
Bradshaw, Robert A.; Dunn, Paul P.J.
Source:
Journal of Immunological Methods 2017
ISSN:
0022-1759
Subject:
genotyping,   etc   ; HLA antigens; alleles; loci;     Show all 4 Subjects
Abstract:
... We have developed a high resolution sequencing based typing method for genotyping Human Leukocyte Antigens (HLA) over a period of twenty years. The methods are based upon the separation of HLA alleles per locus at the initial amplification to simplify the analysis post-sequencing. The increasing discovery of polymorphism in HLA, manifested in new alleles, has necessitated the continuing developmen ...
DOI:
10.1016/j.jim.2017.02.011

16. The effect of the H−1 scaling factors τ and ω on the structure of H in the single-step procedure

Author:
Martini, Johannes W. R.; Schrauf, Matias F.; Garcia-Baccino, Carolina A.; Pimentel, Eduardo C. G.; Munilla, Sebastian; Rogberg-Muñoz, Andres; Cantet, Rodolfo J. C.; Reimer, Christian; Gao, Ning; Wimmer, Valentin; Simianer, Henner
Source:
Genetics, selection, evolution 2018 v.50 no.1 pp. 16
ISSN:
1297-9686
Subject:
genotyping,   etc   ; data collection; equations; genomics; models; variance covariance matrix; wheat;     Show all 7 Subjects
Abstract:
... BACKGROUND: The single-step covariance matrix H combines the pedigree-based relationship matrix [Formula: see text] with the more accurate information on realized relatedness of genotyped individuals represented by the genomic relationship matrix [Formula: see text]. In particular, to improve convergence behavior of iterative approaches and to reduce inflation, two weights [Formula: see text] and ...
DOI:
10.1186/s12711-018-0386-x

17. Validation of intra- and inter-laboratory reproducibility of the Xpert HPV assay according to the international guidelines for cervical cancer screening

Author:
Akbari, Ajmal; Vanden Broeck, Davy; Benoy, Ina; Padalko, Elizaveta; Bogers, Johannes; Arbyn, Marc
Source:
Virology journal 2018 v.15 no.1 pp. 166
ISSN:
1743-422X
Subject:
genotyping,   etc   ; DNA; Papillomaviridae; confidence interval; guidelines; screening; uterine cervical neoplasms;     Show all 7 Subjects
Abstract:
... BACKGROUND: Cervical cancer screening with assays detecting DNA of high-risk human papillomavirus (hrHPV) types is more effective than cytology-based screening. This study completes the diagnostic accuracy assessment conducted previously within the framework of VALGENT-2 (Validation of HPV genotyping Tests) and aims to determine whether the reproducibility of Xpert HPV is in line with internationa ...
DOI:
10.1186/s12985-018-1076-6

18. Deep Learning for Plant Stress Phenotyping: Trends and Future Perspectives

Author:
Singh, Asheesh Kumar; Ganapathysubramanian, Baskar; Sarkar, Soumik; Singh, Arti
Source:
Trends in plant science 2018 v.23 no.10 pp. 883-898
ISSN:
1360-1385
Subject:
genotyping,   etc   ; artificial intelligence; data collection; phenotype; plant stress; prediction;     Show all 6 Subjects
Abstract:
... Deep learning (DL), a subset of machine learning approaches, has emerged as a versatile tool to assimilate large amounts of heterogeneous data and provide reliable predictions of complex and uncertain phenomena. These tools are increasingly being used by the plant science community to make sense of the large datasets now regularly collected via high-throughput phenotyping and genotyping. We review ...
DOI:
10.1016/j.tplants.2018.07.004

19. Genomic characterization of GII.3 noroviruses isolated from children in Zhengzhou city, China, 2015/16

Author:
Liu, Jinjin; Li, Sanjing; Wang, Chao; Zheng, Lijun; Ma, Jie; Li, Chunwei; Huo, Yuqi; Wang, Yumei
Source:
Archives of virology 2018 v.163 no.10 pp. 2737-2742
ISSN:
0304-8608
Subject:
genotyping,   etc   ; Norovirus; children; feces; gastroenteritis; genomics; nucleotide sequences; phylogeny; China;     Show all 9 Subjects
Abstract:
... In this study, we isolated, amplified and sequenced GII.3 norovirus (NoV) strains from children admitted to a department of pediatric gastroenterology presenting with acute gastroenteritis from September 2015 to March 2016. A total of 35 stool samples were collected and eight were GII.3 NoV positive, based on sequencing. The complete genome sequences were determined for two strains while partial g ...
DOI:
10.1007/s00705-018-3905-8

20. Cryptic natural hybridization between two species of Protea

Author:
Mitchell, N.; Holsinger, K.E.
Source:
South African journal of botany 2018 v.118 pp. 306-314
ISSN:
0254-6299
Subject:
genotyping by sequencing,   etc   ; Protea; introgression; mountains; seedlings; single nucleotide polymorphism;     Show all 6 Subjects
Abstract:
... Protea punctata and P. venusta are closely related, but morphologically distinct, species that naturally hybridize in the wild. Here we examined patterns of hybridization and cryptic introgression in seedlings grown from seeds collected at Blesberg Mountain in the Swartberg Mountain range. We used restriction site associated genotyping by sequencing (RAD-Seq) to identify 7185 single nucleotide pol ...
DOI:
10.1016/j.sajb.2017.12.002