scholarly journals Sex matters in Massive Parallel Sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

2016 ◽  
Author(s):  
Laura Benestan ◽  
Jean-Sébastien Moore ◽  
Ben J. G. Sutherland ◽  
Jérémy Le Luyer ◽  
Halim Maaroufi ◽  
...  
Keyword(s):  
Sex Ratio ◽  
Genetic Differentiation ◽  
Massively Parallel Sequencing ◽  
Salvelinus Alpinus ◽  
Genetic Parameter ◽  
Homarus Americanus ◽  
Arctic Char ◽  
Accurate Estimation ◽  
Sequencing Data ◽  
Parallel Sequencing

AbstractUsing massively parallel sequencing data from two species with different life history traits -- American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus) -- we highlighted how an unbalanced sex ratio in the samples combined with a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Multivariate analyses revealed two genetic clusters that separated males and females instead of showing the expected pattern of genetic differentiation among ecologically divergent (inshore vs. offshore in lobster) or geographically distant (east vs. west in Arctic Char) sampling locations. We created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups, and then demonstrated that significant genetic differentiation could be observed despite panmixia for lobster, and that Fst values were overestimated for Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to nonsignificant genetic structure (lobster) and a more accurate estimation of Fst (Arctic Char). We further characterized the putative functions of sex-linked markers. Given that only 9.6% of all marine/diadromous population genomic studies to date reported sex information, we urge researchers to collect and consider individual sex information. In summary, we argue that sex information is useful to (i) control sex ratio in sampling, (ii) overcome “sex-ratio bias” that can lead to spurious genetic differentiation signals and (iii) fill knowledge gaps regarding sex determining systems.

scholarly journals Noninvasive Prenatal Diagnosis of Monogenic Diseases by Targeted Massively Parallel Sequencing of Maternal Plasma: Application to β-Thalassemia

2012 ◽  
Vol 58 (10) ◽  
pp. 1467-1475 ◽  
Author(s):  
Kwan-Wood G Lam ◽  
Peiyong Jiang ◽  
Gary J W Liao ◽  
K C Allen Chan ◽  
Tak Y Leung ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Massively Parallel Sequencing ◽  
Globin Gene ◽  
Maternal Plasma ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Plasma Dna ◽  
Parallel Sequencing ◽  
Noninvasive Prenatal Diagnosis ◽  
Monogenic Diseases

Abstract BACKGROUND A genomewide genetic and mutational profile of a fetus was recently determined via deep sequencing of maternal plasma DNA. This technology could have important applications for noninvasive prenatal diagnosis (NIPD) of many monogenic diseases. Relative haplotype dosage (RHDO) analysis, a core step of this procedure, would allow one to elucidate the maternally inherited half of the fetal genome. For clinical applications, the cost and complexity of data analysis might be reduced via targeted application of this approach to selected genomic regions containing disease-causing genes. There is thus a need to explore the feasibility of performing RHDO analysis in a targeted manner. METHODS We performed target enrichment by using solution-phase hybridization followed by massively parallel sequencing of the β-globin gene region in 2 families undergoing prenatal diagnosis for β-thalassemia. We used digital PCR strategies to physically deduce parental haplotypes. Finally, we performed RHDO analysis with target-enriched sequencing data and parental haplotypes to reveal the β-thalassemic status for the fetuses. RESULTS A mean sequencing depth of 206-fold was achieved in the β-globin gene region by targeted sequencing of maternal plasma DNA. RHDO analysis was successful for the sequencing data obtained from the target-enriched samples, including a region in one of the families in which the parents had similar haplotype structures. Data analysis revealed that both fetuses were heterozygous carriers of β-thalassemia. CONCLUSIONS Targeted sequencing of maternal plasma DNA for NIPD of monogenic diseases is feasible.

scholarly journals SICTIN: Rapid footprinting of massively parallel sequencing data

2010 ◽  
Vol 3 (1) ◽  
Author(s):  
Stefan Enroth ◽  
Robin Andersson ◽  
Claes Wadelius ◽  
Jan Komorowski
Keyword(s):  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Parallel Sequencing

scholarly journals Detection of CYP2C19 Genetic Variants in Malaysian Orang Asli from Massively Parallel Sequencing Data

PLoS ONE ◽  
2016 ◽  
Vol 11 (10) ◽  
pp. e0164169 ◽  
Author(s):  
Geik Yong Ang ◽  
Choo Yee Yu ◽  
Vinothini Subramaniam ◽  
Mohd Ikhmal Hanif Abdul Khalid ◽  
Tuan Azlin Tuan Abdu Aziz ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Parallel Sequencing ◽  
Orang Asli

scholarly journals Genetic Stock Identification and Relative Contribution of Arctic Char (Salvelinus alpinus) from the Hornaday and Brock Rivers to Subsistence Fisheries in Darnley Bay, Northwest Territories + Supplementary Appendix Tables S1 to S4 (See Article Tools)

ARCTIC ◽  
2016 ◽  
Vol 69 (3) ◽  
pp. 231
Author(s):  
Les N. Harris ◽  
David A. Bogsuski ◽  
Colin P. Gallagher ◽  
Kimberly L. Howland
Keyword(s):  
Life History ◽  
Genetic Differentiation ◽  
Salvelinus Alpinus ◽  
Canadian Arctic ◽  
Arctic Char ◽  
Genetic Stock ◽  
Subsistence Fisheries ◽  
Bay Area ◽  
Sampling Locations ◽  
Mixed Stock

Where anadromous fishes occur in the Canadian Arctic, they provide the mainstay of local subsistence fisheries of varying intensities. Many of these fisheries harvest a mixture of stocks at discrete locations and it is often not known which stocks, specifically, are being harvested and to what extent. In the Darnley Bay area of the Northwest Territories, Arctic char, Salvelinus alpinus, in particular have long provided an important subsistence resource to residents of Paulatuk, and char from two systems (the Hornaday and Brock Rivers) are thought to contribute to the coastal fishery for this species. Genetic mixed-stock analysis (GMA) is routinely applied for resolving stock contributions to such fisheries, yet studies incorporating GMA to understand specifically which stocks are being harvested in the Canadian Arctic, and to what extent, are relatively scarce. In this study, we assayed microsatellite DNA variation among 987 Arctic char from two important coastal subsistence fisheries and several inland sampling locations in the Darnley Bay area to (1) assess the degree of genetic structuring between the Hornaday and Brock Rivers and (2) resolve the proportional contributions of these stocks to coastal mixed-stock fisheries in the region using GMA. Overall, genetic differentiation was relatively high and significant (θ = 0.117; 95% C.I. = 0.097–0.142) among baseline sampling locations. Overall patterns of genetic stock structure also support previous hypotheses that additional life history types (e.g., landlocked or freshwater-resident char, or both) exist in the Hornaday system, as indicated by elevated levels of genetic differentiation between some of our sampling locations. The GMA suggested that, while both river systems contribute to the coastal fishery, catches were dominated by Arctic char from the Hornaday River, which highlights the importance of this system. All told, our results may be relevant to the management of the subsistence fishery in Darnley Bay and for furthering the collective understanding of char biodiversity and life history variation in the Canadian Arctic.

Hunger and the Capture of Grayling and Char

1974 ◽  
Vol 31 (12) ◽  
pp. 1945-1948 ◽  
Author(s):  
J. E. Bryan
Keyword(s):  
Sex Ratio ◽  
Salvelinus Alpinus ◽  
Yukon Territory ◽  
Arctic Char ◽  
Remote Areas ◽  
Size Selection ◽  
Arctic Grayling ◽  
Thymallus Arcticus

Arctic grayling, Thymallus arcticus, and Arctic char, Salvelinus alpinus, were collected by angling and seining in remote areas of northern Yukon Territory. Stomach samples were observed to test the hypothesis that fish caught by angling had eaten less food than those caught by seining. The hypothesis was supported by the data for grayling. The data for char were consistent with the hypothesis, but the results were not statistically significant. There was no difference in the sex ratio of fish caught by the two methods. Angling selected larger char than did seining, but there was no evidence of size selection in grayling.

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