Bioinformatics analysis of whole genome resequencing data in the chicken

One of the most important challenges in human medicine is the identification of genetic variants underlying complex diseases but we are still not able to assess the risk of disease by genetic profiling. Also, as the complete functional properties remain unknown for most genes it is very important to further functionally annotate genomes. The large abundance of domestic animals kept by humans constitute a valuable asset for the identification of genetic elements involved in complex disease and to unravel gene functions. Advantages of using animal models in studies of complex traits include the possibilities to strictly control environmental variation and to perform invasive measurements. Domestic animals have the additional advantage that different breeds segregate for traits of importance to human diseases. Massive parallel sequencing technology (NextGen) enables researchers to resequence already completed genomes and enables whole-genome sequence information from multiple DNA samples to be determined in a short time. This makes it possible to, in a global manner, determine the extent of sequence polymorphisms among members within a species. Insertions and deletions are among the structural variation events that may be responsible for the variation in the expression of traits related to growth and reproduction in chickens. Rubin et al. (2010) pioneered the use of NextGen sequencing for population-based studies. The current study presented here will now extend previous analysis performed by Rubin et al., 2010 using paired reads, which makes identification of insertions/deletions in the chicken genome possible. Chicken lines whose sequences have been analyzed in this study include the red junglefowl as a reference bird, the High growth line (HL), the low growth line (LL) both established from White Plymouth Rock chickens in 1957 (Dunnington and Siegel, 1996) and the White Leghorn line L13 (WL_L13). Whole genome resequencing was performed on three lines of chickens where genomic DNA from 11 chicken individuals were pooled from each line to generate paired-end reads. Paired-end reads of 50 bp each were generated using AB-SOLiDTM v3.0. The overall coverage of the reads was 20-25x. Most deletions were found for sizes ranging from 4kbp to 10kbp in the HL, LL and the WL_L13 and most insertions were detected for size ranging from 1.1kbp to 3.1kbp. The coverage from matching pipeline was performed on chromosome 13 that contains 326 regions detected as deletions using mate-pair reads. The identified deletions overlapping duplicated regions in the chicken genome were removed for chromosome 13 in HL and considering a median coverage equal to zero (of reads mapped by the matching pipeline) in putative deleted regions detected using paired reads resulted in 73 deleted regions. It is possible that most of the identified deletions are false positives and further refinement in the approach is required to increase the probability of finding only true deletions and insertions as well. This could be due to the artifacts in the library as well as the in the assembly of the sequenced chicken genome. Further analysis can be carried out to find the exact breakpoints of the deletions. We suggest the approach of taking the set of reads that are unmapped in the genome and align them again by splitting those into two parts and allowing a gap or an insertion between them, as reads spanning these features should be present in the genomes of populations bearing true deletions and insertions, respectively

Impact of Terrorism on Stock Market: A Case of South Asian Stock Markets

The purpose of this study is to examine the impact of terrorism on stock markets of South Asia namely, Karachi Stock Exchange 100 index (Pakistan), Bombay Stock Exchange (India), Colombo Stock Exchange (Sri Lanka) and Chittagong Stock Exchange (Bangladesh). Monthly panel data has been used for the period of January 2000 to December 2016. Terrorism events happened during the period of 2000 to 2016 have been incorporated to examine the impact of terrorism on stock market returns of South Asia. DCC GARCH through R software is used to analyze the impact of terrorism on stock market returns and to analyze the spillover effect of terrorism in one country and on the stock markets of other countries of South Asia. The results indicate that terrorism has significant and negative effect on stock market returns of Pakistan, India and Bangladesh but insignificant in Sri Lanka. Results also shows that stock markets return of Pakistan, India, and Bangladesh are significant and positively correlated with each other except the Stock market of Sri Lanka

Genetics of adaptation in modern chicken

This work is licensed under a Creative Commons Attribution 4.0 International License.We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5×10−6). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding

Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia

IntroductionThe suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods.MethodsFor this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL.ResultsBoth the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions.DiscussionThe filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL

Effects of a high-dose 24-h infusion of tranexamic acid on death and thromboembolic events in patients with acute gastrointestinal bleeding (HALT-IT): an international randomised, double-blind, placebo-controlled trial

Background: Tranexamic acid reduces surgical bleeding and reduces death due to bleeding in patients with trauma. Meta-analyses of small trials show that tranexamic acid might decrease deaths from gastrointestinal bleeding. We aimed to assess the effects of tranexamic acid in patients with gastrointestinal bleeding. Methods: We did an international, multicentre, randomised, placebo-controlled trial in 164 hospitals in 15 countries. Patients were enrolled if the responsible clinician was uncertain whether to use tranexamic acid, were aged above the minimum age considered an adult in their country (either aged 16 years and older or aged 18 years and older), and had significant (defined as at risk of bleeding to death) upper or lower gastrointestinal bleeding. Patients were randomly assigned by selection of a numbered treatment pack from a box containing eight packs that were identical apart from the pack number. Patients received either a loading dose of 1 g tranexamic acid, which was added to 100 mL infusion bag of 0·9% sodium chloride and infused by slow intravenous injection over 10 min, followed by a maintenance dose of 3 g tranexamic acid added to 1 L of any isotonic intravenous solution and infused at 125 mg/h for 24 h, or placebo (sodium chloride 0·9%). Patients, caregivers, and those assessing outcomes were masked to allocation. The primary outcome was death due to bleeding within 5 days of randomisation; analysis excluded patients who received neither dose of the allocated treatment and those for whom outcome data on death were unavailable. This trial was registered with Current Controlled Trials, ISRCTN11225767, and ClinicalTrials.gov, NCT01658124. Findings: Between July 4, 2013, and June 21, 2019, we randomly allocated 12 009 patients to receive tranexamic acid (5994, 49·9%) or matching placebo (6015, 50·1%), of whom 11 952 (99·5%) received the first dose of the allocated treatment. Death due to bleeding within 5 days of randomisation occurred in 222 (4%) of 5956 patients in the tranexamic acid group and in 226 (4%) of 5981 patients in the placebo group (risk ratio [RR] 0·99, 95% CI 0·82–1·18). Arterial thromboembolic events (myocardial infarction or stroke) were similar in the tranexamic acid group and placebo group (42 [0·7%] of 5952 vs 46 [0·8%] of 5977; 0·92; 0·60 to 1·39). Venous thromboembolic events (deep vein thrombosis or pulmonary embolism) were higher in tranexamic acid group than in the placebo group (48 [0·8%] of 5952 vs 26 [0·4%] of 5977; RR 1·85; 95% CI 1·15 to 2·98). Interpretation: We found that tranexamic acid did not reduce death from gastrointestinal bleeding. On the basis of our results, tranexamic acid should not be used for the treatment of gastrointestinal bleeding outside the context of a randomised trial

Bioinformatic analysis of whole genome sequencing data

Evolution has shaped the life forms for billion of years. Domestication is an accelerated process that can be used as a model for evolutionary changes. The aim of this thesis project has been to carry out extensive bioinformatic analyses of whole genome sequencing data to reveal SNPs, InDels and selective sweeps in the chicken, pig and dog genome. Pig genome sequencing revealed loci under selection for elongation of back and increased number of vertebrae, associated with the NR6A1, PLAG1, and LCORL genes. The scan for copy number variations (CNVs) revealed four duplications at the KIT locus associated with dominant white and belt colour phenotypes. Selective sweeps in the dog genome included genes involved in adaptation to a starch rich diet, fat metabolism and behavior. Identification of a selective sweep and a CNV in the AMY2B gene, which correlates with variation in α-amylase expression, along with selective sweeps in MGAM and SGLT1, in dogs revealed adaptation to a starch-rich diet after domestication. Analysis of chicken genome resequencing data identified hundreds of regions under selection shared among all domestic chicken and others that were specific for layers or broiler chickens and 68 fixed large deletions and 70 small InDels in domestic chicken populations. Structural variations are changes in the genome that may affect the copy number of genes, their regulation or their coding sequence. Current methods utilize sequence information from either single sample or pair of samples to scan for CNVs across the genome. We developed a fast algorithm and a tool, MultiSV, to identify structural variations using short reads from massively parallel sequencing of multiple populations. This thesis demonstrates the importance of structural variations as a factor contributing to phenotypic diversity in domestic animals and has revealed regions under strong selection during animal domestication and breeding. It also presents a new method for the identification of structural variations in populations using short reads from NextGen sequencers

Metastatic prostate tumor to testes: Sign of advance disease

Prostate cancer is the second most common cause of mortality for males in the United States. Metastases may be present, typically in the axial skeletal region. To date, few patients have presented with metastases to the testicles. We present the case of an adult male with diagnosed prostate cancer who presented and subsequently diagnosed bilateral testicular metastases. Testicular metastases secondary to diagnosed prostate cancer are very rare. Patients present with these metastases may have unfavorable prognosis. This case demonstrates that prostate cancer may metastasize to rare locations such as the testes, requiring further surgical intervention

Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants

Background Oesophageal atresia (OA) is a life-threatening developmental defect characterized by a lost continuity between the upper and lower oesophagus. The most common form is a distal connection between the trachea and the oesophagus, i.e. a tracheoesophageal fistula (TEF). The condition may be part of a syndrome or occurs as an isolated feature. The recurrence risk in affected families is increased compared to the population-based incidence suggesting contributing genetic factors. Methods To gain insight into gene variants and genes associated with isolated OA we conducted whole genome sequencing on samples from three families with recurrent cases affected by congenital and isolated TEF. Results We identified a combination of single nucleotide variants (SNVs), splice site variants (SSV) and structural variants (SV) annotated to altogether 100 coding genes in the six affected individuals. Conclusion This study highlights rare SVs among candidate gene variants in our individuals with OA and provides a gene framework for further investigations of genetic factors behind this malformation

Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a heterogeneous neuropsychiatric disorder with a complex genetic background. Analysis of altered molecular processes in ASD patients requires linear and nonlinear methods that provide interpretable solutions. Interpretable machine learning provides legible models that allow explaining biological mechanisms and support analysis of clinical subgroups. In this work, we investigated several case-control studies of gene expression measurements of ASD individuals. We constructed a rule-based learning model from three independent datasets that we further visualized as a nonlinear gene-gene co-predictive network. To find dissimilarities between ASD subtypes, we scrutinized a topological structure of the network and estimated a centrality distance. Our analysis revealed that autism is the most severe subtype of ASD, while pervasive developmental disorder-not otherwise specified and Asperger syndrome are closely related and milder ASD subtypes. Furthermore, we analyzed the most important ASD-related features that were described in terms of gene co-predictors. Among others, we found a strong co-predictive mechanism between EMC4 and TMEM30A, which may suggest a co-regulation between these genes. The present study demonstrates the potential of applying interpretable machine learning in bioinformatics analyses. Although the proposed methodology was designed for transcriptomics data, it can be applied to other omics disciplines

Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.

Background: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome. Results: We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split. Conclusions: We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation