Genome-wide Analysis Study Research Articles

SUN-201 GENOME WIDE ANALYSIS STUDY TO EVALUATE POTENTIAL GENETIC RISKS AND IMMUNOLOGICAL PATHWAYS ASSOCIATED WITH CHRONIC KIDNEY DISEASE OF UNKNOWN ETIOLOGY

Chronic kidney disease of unknown etiology (CKDu) has been studied on the light of its etiology and pathogenesis, mostly on possible involvement of environmental factors. Earlier inconsistent data on involvement of different heavy metals has been suggested along with plausible roles of herbicides, mycotoxins, pesticides, and algal toxins with CKDu. The present study is proposed to identify exact cause(s) of CKDu and complex involvement of genetic and environmental factors.This study has evaluated the potential candidate genes associated with CKDu through a genome wide analysis study (GWAS

A Case-Control Study to Evaluate the Etiology of Esophageal Cancer in Tanzania

Abstract 75 Objective: East Africa has been previously reported as a geographic area with a disproportionately high incidence of squamous cell esophageal cancer (EC). In the setting of an apparent geographic cluster, we sought to identify specific etiologic factors contributing to the high incidence of EC in Tanzania (TZ). Methods: We performed a case-control study to examine possible associations between EC and selected environmental, dietary, and lifestyle factors. Newly diagnosed EC cases were recruited at Muhimbili National Hospital and Ocean Road Cancer Institute during 2014-2015. Hospital controls were identified from patients with non-malignant conditions and matched 1:1 for gender and age ±10 years. The study team conducted in-person interviews. A matched case-control analysis used McNemar’s test with a Mantel-Haenszel estimate for odds ratios (OR). Results: 375 cases and 375 controls were enrolled. 71% of cases and controls were male. Median age was 58 years (range 30-91) for cases and 55 years (range 31-88) for controls. Among cases with a confirmed pathologic diagnosis, squamous cell carcinoma was the most common histology (85%). Liquor consumption (OR 1.84, 95% CI: 1.05-3.22, p=0.04), burning firewood (OR 2.66, 95% CI: 1.88-3.76, p<0.001), use of kerosene (OR 3.29, 95% CI: 2.36-4.59, p<0.001), and use of surface water as a primary source of drinking water (OR 2.3, 95% CI: 1.41-3.76, p=0.001) were associated with increased risk of EC. Running water, gas, and electric utilities in the household were protective. Conclusion: Alcohol consumption, firewood and kerosene use as fuel, and surface water consumption merit further investigation as potential etiologic factors contributing to high EC incidence in TZ. Future research will include conducting multivariate analysis with these and other potential risk factors and a genome-wide analysis study using DNA extracted from saliva specimens obtained from cases and controls. Funding: Research support provided by the National Cancer Institute, National Institutes of Health Contract No. HH5N261200800001E. AUTHORS’ DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST: Elia Mmbaga No relationship to disclose Katrina Deardorff No relationship to disclose Beatrice Mushi No relationship to disclose Li Zhang No relationship to disclose William Mgisha No relationship to disclose Aparna Parikh Employment: Genentech Stock or Other Ownership: Genentech Travel, Accommodations, Expenses: Genentech Robert A. Hiatt No relationship to disclose Julius Mwaiselage No relationship to disclose Katherine Van Loon Consulting or Advisory Role: Bayer Company: OncoPlex Diagnostics

Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress

Dairy cows with increased rectal temperature experience lower milk yield and fertility. Rectal temperature during heat stress is heritable, so genetic selection for body temperature regulation could reduce effects of heat stress on production. One aim of the study was to validate the relationship between genotype and heat tolerance for single nucleotide polymorphisms (SNPs) previously associated with resistance to heat stress. A second aim was to identify new SNPs associated with heat stress resistance. Thermotolerance was assessed in lactating Holsteins during the summer by measuring rectal temperature (a direct measurement of body temperature regulation; n = 435), respiration rate (an indirect measurement of body temperature regulation, n = 450) and sweating rate (the major evaporative cooling mechanism in cattle, n = 455). The association between genotype and thermotolerance was evaluated for 19 SNPs previously associated with rectal temperature from a genomewide analysis study (GWAS), four SNPs previously associated with change in milk yield during heat stress from GWAS, 2 candidate gene SNPs previously associated with rectal temperature and respiration rate during heat stress (ATPA1A and HSP70A) and 66 SNPs in genes previously shown to be associated with reproduction, production or health traits in Holsteins. For SNPs previously associated with heat tolerance, regions of BTA4, BTA6 and BTA24 were associated with rectal temperature; regions of BTA6 and BTA24 were associated with respiration rate; and regions of BTA5, BTA26 and BTA29 were associated with sweating rate. New SNPs were identified for rectal temperature (n = 12), respiration rate (n = 8) and sweating rate (n = 3) from among those previously associated with production, reproduction or health traits. The SNP that explained the most variation were PGR and ASL for rectal temperature, ACAT2 and HSD17B7 for respiration rate, and ARL6IP1 and SERPINE2 for sweating rate. ARL6IP1 was associated with all three thermotolerance traits. In conclusion, specific genetic markers responsible for genetic variation in thermoregulation during heat stress in Holsteins were identified. These markers may prove useful in genetic selection for heat tolerance in Holstein cattle.

Global distribution of polymorphisms associated with delayed Plasmodium falciparum parasite clearance following artemisinin treatment: Genotyping of archive blood samples

The recent emergence and spread of artemisinin-resistant Plasmodium falciparum isolates is a growing concern for global malaria-control efforts. A recent genome-wide analysis study identified two SNPs at genomic positions MAL10-688956 and MAL13-1718319, which are linked to delayed clearance of parasites following artemisinin combination therapy (ACT). It is expected that continuous artemisinin pressure will affect the distribution of these SNPs. Here, we investigate the worldwide distribution of these SNPs using a large number of archived samples in order to generate baseline data from the period before the emergence of ACT resistance. The presence of SNPs in MAL10-688956 and MAL13-1718319 was assessed by nested PCR RFLP and direct DNA sequencing using 653 global P. falciparum samples obtained before the reported emergence of ACT resistance. SNPs at MAL10-688956 and MAL13-1718319 associated with delayed parasite clearance following ACT administration were observed in 8% and 3% of parasites, respectively, mostly in Cambodia and Thailand. Parasites harbouring both SNPs were found in only eight (1%) isolates, all of which were from Cambodia and Thailand. Linkage disequilibrium was detected between MAL10-688956 and MAL13-1718319, suggesting that this SNP combination may have been selected by ACT drug pressure. Neither of the SNPs associated with delayed parasite clearance were observed in samples from Africa or South America. Baseline information of the geographical difference of MAL10-688956 and MAL13-1718319 SNPs provides a solid basis for assessing whether these SNPs are selected by artemisinin-based combination therapies.

Attention-Deficit/Hyperactivity Disorder Polygenic Risk Scores Predict Attention Problems in a Population-Based Sample of Children

Clinically, attention-deficit/hyperactivity disorder (ADHD) is characterized by hyperactivity, impulsivity, and inattention and is among the most common childhood disorders. These same traits that define ADHD are variable in the general population, and the clinical diagnosis may represent the extreme end of a continuous distribution of inattentive and hyperactive behaviors. This hypothesis can be tested by assessing the predictive value of polygenic risk scores derived from a discovery sample of ADHD patients in a target sample from the general population with continuous scores of inattention and hyperactivity. In addition, the genetic overlap between ADHD and continuous ADHD scores can be tested across rater and age. The Psychiatric Genomics Consortium has performed the largest genome-wide analysis (GWA) study of ADHD so far, including 5,621 clinical patients and13,589 controls. The effects sizes of single nucleotide polymorphisms (SNPs) estimated inthis meta-analysis were used to obtain individual polygenic risk scores in an independentpopulation-based cohort of 2,437 children from the Netherlands Twin Register. The variance explained in Attention Problems (AP) scale scores by the polygenic risk scores wasestimated bylinear mixed modeling. The ADHD polygenic risk scores significantly predicted both parent and teacher ratings of AP in preschool- and school-aged children. These results indicate genetic overlap between a diagnosis of ADHD and AP scale scores across raters and age groups and provides evidence for a dimensional model of ADHD. Future GWA studies on ADHD can likely benefit from the inclusion of population-based cohorts and the analysis of continuous scores.

Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza

The over-expression of plant specific SnRK2 gene family members by hyperosmotic stress and some by abscisic acid is well established. In this report, we have analyzed the evolution of SnRK2 gene family in different plant lineages including green algae, moss, lycophyte, dicot and monocot. Our results provide some evidences to indicate that the natural selection pressure had considerable influence on cis-regulatory promoter region and coding region of SnRK2 members in Arabidopsis and Oryza independently through time. Observed degree of sequence/motif conservation amongst SnRK2 homolog in all the analyzed plant lineages strongly supported their inclusion as members of this family. The chromosomal distributions of duplicated SnRK2 members have also been analyzed in Arabidopsis and Oryza. Massively Parallel Signature Sequencing (MPSS) database derived expression data and the presence of abiotic stress related promoter elements within the 1kb upstream promoter region of these SnRK2 family members further strengthen the observations of previous workers. Additionally, the phylogenetic relationships of SnRK2 have been studied in all plant lineages along with their respective exon–intron structural patterns. Our results indicate that the ancestral SnRK2 gene of land plants gradually evolved by duplication and diversification and modified itself through exon–intron loss events to survive under environmental stress conditions.

Genome‐wide association study of body mass index in 23 000 individuals with and without asthma

Both asthma and obesity are complex disorders that are influenced by environmental and genetic factors. Shared genetic factors between asthma and obesity have been proposed to partly explain epidemiological findings of co-morbidity between these conditions. To identify genetic variants that are associated with body mass index (BMI) in asthmatic children and adults, and to evaluate if there are differences between the genetics of BMI in asthmatics and healthy individuals. In total, 19 studies contributed with genome-wide analysis study (GWAS) data from more than 23 000 individuals with predominantly European descent, of whom 8165 are asthmatics. We report associations between several DENND1B variants (P = 2.2 × 10(-7) for rs4915551) on chromosome 1q31 and BMI from a meta-analysis of GWAS data using 2691 asthmatic children (screening data). The top DENND1B single nucleotide polymorphisms(SNPs) were next evaluated in seven independent replication data sets comprising 2014 asthmatics, and rs4915551 was nominally replicated (P < 0.05) in two of the seven studies and of borderline significance in one (P = 0.059). However, strong evidence of effect heterogeneity was observed and overall, the association between rs4915551 and BMI was not significant in the total replication data set, P = 0.71. Using a random effects model, BMI was overall estimated to increase by 0.30 kg/m(2) (P = 0.01 for combined screening and replication data sets, N = 4705) per additional G allele of this DENND1BSNP. FTO was confirmed as an important gene for adult and childhood BMI regardless of asthma status. DENND1B was recently identified as an asthma susceptibility gene in a GWAS on children, and here, we find evidence that DENND1B variants may also be associated with BMI in asthmatic children. However, the association was overall not replicated in the independent data sets and the heterogeneous effect of DENND1B points to complex associations with the studied diseases that deserve further study.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

Genome-wide association study of survival in small cell lung cancer patients treated with irinotecan and cisplatin chemotherapy.

7089 Background: The prognosis of patients with extensive-disease small-cell lung cancer (ED-SCLC) remains poor. Despite a high initial response rate to chemotherapy, most patients die from rapid recurrence. We conducted a genome-wide analysis study (GWAS) to examine whether germline genetic variations are prognostic factors in ED-SCLC patients treated with irinotecan and cisplatin (IP) chemotherapy. Methods: We prospectively collected blood samples from 139 patients who participated in two phase II studies of IP chemotherapy as first-line therapy and conducted a GWAS using overall survival (OS) as the endpoint. Germline DNA was genotyped using the Affymetrix 5.0 or 6.0 array sets. Associations between OS and single nucleotide polymorphisms (SNPs) were investigated using multivariate Cox regression analysis. Adjustments for age, performance status (PS) and gender were made. We selected most promising SNPs with p&lt;1×10−6 in the GWAS allelic association analyses. Results: A total of 426,019 SNPs were genotyped and 343,530 SNPs passed quality control (HWE, p&lt;10-7, minor allele frequency&gt;1%). We found 7 SNPs showing a significant association with OS. Patients harboring rs16950650 CT, rs7186128 AG or GG, rs17574269 AG, rs8020368 CC, rs4655567 CC, rs2166219 TT and rs2018683 TT genotypes showed shorter OS compared to patients with control alleles. Hazards ratios of death for each risk variants were 30.2 (95% CI, 8.3-109.0, p=2.1X10-7), 2.5 (95% CI, 1.7-3.5, p=3.8X10-7), 7.6 (95% CI, 3.4-16.6, p=4.5X10-7), 3.4 (95% CI, 2.1-5.5, p=3.5X10-7), 4.9 (95% CI, 2.7-9.0, p=3.1X10-7), 5.8 (95% CI, 2.9-11.7, p=8.4X10-7) and 7.8 (95% CI, 3.4-17.7, p=8.0X10-7), respectively. Among these SNPs, rs4655567, rs8020368, rs2018683 and rs17574269 were significantly associated with a refractory relapse. In multivariate logistic analysis including age, gender and PS, rs8020368 CC genotype showed higher risk of refractory relapse than patients with TT or TC genotype (HR=14.9 [95% CI, 1.9-114.8], p=0.010). Conclusions: This exploratory GWAS identified several candidate SNPs that might predictive for the outcome of patients with ED-SCLC receiving IP chemotherapy.

Actin-related protein 2/3 complex subunit 5 (ARPC5) contributes to cell migration and invasion and is directly regulated by tumor-suppressive microRNA-133a in head and neck squamous cell carcinoma

Our expression signatures of human cancers including head and neck squamous cell carcinoma (HNSCC) demonstrated that downregulation of microRNA-133a (miR-133a) were frequently observed in cancer cells. The restoration of miR-133a in cancer cells revealed that it functions as a tumor suppressor. In this study, we investigated the novel molecular targets of miR-133a in HNSCC cancer cells and its oncogenic function, especially as it contributes to cancer cell migration and invasion. The genome-wide gene expression analysis and bioinformatics study showed that actin-related protein 2/3 complex subunit 5 (ARPC5) is a candidate target of miR-133a. Furthermore, luciferase reporter assay demonstrated that ARPC5 is directly regulated by miR-133a. Silencing of ARPC5 revealed significant inhibition of cell migration and invasion in HNSCC cell lines, SAS, HSC3 and IMC-3. In HSC3 cells, restoration of miR-133a or silencing ARPC5 led to a reorganization of the actin cytoskeleton and a subsequent change in cell morphology to a round, bleb-like shape. The expression levels of ARPC5 were significantly higher in HNSCC tissues than in non-cancer tissues. Immunohistochemistry showed that the levels of ARPC5 expression were significantly higher in invasive cancer cells. ARPC5 contributed to cancer cell migration and invasion in HNSCC and this gene was directly regulated by miR-133a. Our analysis of novel tumor-suppressive miR‑133a-mediated cancer pathways provides new insights into the potential mechanisms of HNSCC oncogenesis.

Gout and Type 2 diabetes have a mutual inter-dependent effect on genetic risk factors and higher incidences

To explore the causal relationship between gout and Type 2 diabetes based on genetic evidence and national outpatient database. Twenty male gout patients with early-onset, gout family history, without a habit of alcohol consumption or obesity before the first attack of gout were selected from hospital in 2010; and 42 unrelated male Chinese subjects were selected from HapMap as controls for genome-wide analysis study (GWAS). The comorbid diseases with gout were revealed by applying the significant single nucleotide polymorphisms (SNPs) to MetaCore platform, and the comorbid relationship was analysed by standardized incidence ratio (SIR) from outpatient database. A total of 334 SNPs were significantly related to gout in GWAS (P < 10(-7)), and Type 2 diabetes was the most significantly associated disease with gout as recognized by 36 gene symbols correspondent to the above significant SNPs. The analysis of national outpatient database showed that the overall incident Type 2 diabetes was 1.50 cases per 1000 person-months among gout patients, which was higher than the overall incident gout (1.06 cases) among Type 2 diabetes. The age-adjusted SIR of incident Type 2 diabetes among gout was 2.59 (95% CI 2.42, 2.78), whereas the age-adjusted SIR for incident gout among Type 2 diabetes was 1.61 (95% CI 1.48, 1.74). After excluding obesity and alcohol consumption behaviour, this study showed that patients with gout and Type 2 diabetes shared the common genetic factors most, and that there existed a mutual inter-dependent effect on higher incidences.

POPLAR AS A TREE MODEL FOR HORTICULTURE AND BEYOND: A CASE STUDY OF GENOME-SCALE CHANGES IN GENE EXPRESSION DURING BUD ENTRY AND RELEASE FROM DORMANCY

With the available genomic sequence and other experimental attributes, poplar has emerged as a leading candidate to study traits specific to woody perennial plants. Genomic and molecular knowledge gained from studies related to flowering, stem development, tree architecture, phenology and dormancy can be extended readily to woody species in forestry and horticulture. As an example of the value and transferability of poplar genomic studies to tree biology, we conducted a genome-wide transcript analysis study utilizing a NimbleGen microarray representing 65,966 individual gene sequences derived from the poplar genome sequence. The investigation included more than 20 tissue types and several developmental sequences. Presented here is a preliminary analysis of changes in gene expression during entry into and exit from bud dormancy. Potential applications of these data include identification of candidate genes for studying natural polymorphisms, targets for reverse genetic studies, target promoters for control of gene expression, and tools for many forms of marker-aided breeding and genetic engineering of woody plant growth and development.

Multiple Endoplasmic Reticulum-to-Nucleus Signaling Pathways Coordinate Phospholipid Metabolism with Gene Expression by Distinct Mechanisms

In many organisms the coordinated synthesis of membrane lipids is controlled by feedback systems that regulate the transcription of target genes. However, a complete description of the transcriptional changes that accompany the remodeling of membrane phospholipids has not been reported. To identify metabolic signaling networks that coordinate phospholipid metabolism with gene expression, we profiled the sequential and temporal changes in genome-wide expression that accompany alterations in phospholipid metabolism induced by inositol supplementation in yeast. This analysis identified six distinct expression responses, which included phospholipid biosynthetic genes regulated by Opi1p, endoplasmic reticulum (ER) luminal protein folding chaperone and oxidoreductase genes regulated by the unfolded protein response pathway, lipid-remodeling genes regulated by Mga2p, as well as genes involved in ribosome biogenesis, cytosolic stress response, and purine and amino acid metabolism. We also report that the unfolded protein response pathway is rapidly inactivated by inositol supplementation and demonstrate that the response of the unfolded protein response pathway to inositol is separable from the response mediated by Opi1p. These data indicate that altering phospholipid metabolism produces signals that are relayed through numerous distinct ER-to-nucleus signaling pathways and, thereby, produce an integrated transcriptional response. We propose that these signals are generated in the ER by increased flux through the pathway of phosphatidylinositol synthesis.