Genome-wide Single Nucleotide Polymorphism Array Research Articles

The Molecular Landscape of Primary Acral Melanoma: A Multicenter Study of the Italian Melanoma Intergroup (IMI).

Acral melanoma (AM) is a rare and aggressive subtype of melanoma affecting the palms, soles, and nail apparatus with similar incidence among different ethnicities. AM is unrelated to ultraviolet radiation and has a low mutation burden but frequent chromosomal rearrangements and gene amplifications. Next generation sequencing of 33 genes and somatic copy number variation (CNV) analysis with genome-wide single nucleotide polymorphism arrays were performed in order to molecularly characterize 48 primary AMs of Italian patients in association with clinicopathological and prognostic features. BRAF was the most commonly mutated gene, followed by NRAS and TP53, whereas TERT promoter, KIT, and ARID1A were less frequently mutated. Gains and losses were recurrently found in the 1q, 6p, 7, 8q, 20 and 22 chromosomes involving PREX2, RAC1, KMT2C, BRAF, CCND1, TERT, and AKT3 genes, and in the 6q, 9, 10, 11q and 16q chromosomes including CDKN2A, PTEN, and ADAMTS18 genes, respectively. This study confirmed the variety of gene mutations and the high load of CNV in primary AM. Some genomic alterations were associated with histologic prognostic features. BRAF mutations, found with a higher rate than previously reported, correlated with a low Breslow thickness, low mitotic count, low CNV of the AMs, and with early-stage of disease.

An Integrated Clinical and Genetic Prediction Model for Tacrolimus Levels in Pediatric Solid Organ Transplant Recipients.

Background.There are challenges in achieving and maintaining therapeutic tacrolimus levels after solid organ transplantation (SOT). The purpose of this genome-wide association study was to generate an integrated clinical and genetic prediction model for tacrolimus levels in pediatric SOT.Methods.In a multicenter prospective observational cohort study (2015–2018), children <18 years old at their first SOT receiving tacrolimus as maintenance immunosuppression were included (455 as discovery cohort; 322 as validation cohort). Genotyping was performed using a genome-wide single nucleotide polymorphism (SNP) array and analyzed for association with tacrolimus trough levels during 1-y follow-up.Results.Genome-wide association study adjusted for clinical factors identified 25 SNPs associated with tacrolimus levels; 8 were significant at a genome-wide level (P < 1.025 × 10−7). Nineteen SNPs were replicated in the validation cohort. After removing SNPs in strong linkage disequilibrium, 14 SNPs remained independently associated with tacrolimus levels. Both traditional and machine learning approaches selected organ type, age at transplant, rs776746, rs12333983, and rs12957142 SNPs as the top predictor variables for dose-adjusted 36- to 48-h posttacrolimus initiation (T1) levels. There was a significant interaction between age and organ type with rs776476*1 SNP (P < 0.05). The combined clinical and genetic model had lower prediction error and explained 30% of the variation in dose-adjusted T1 levels compared with 18% by the clinical and 12% by the genetic only model.Conclusions.Our study highlights the importance of incorporating age, organ type, and genotype in predicting tacrolimus levels and lays the groundwork for developing an individualized age and organ-specific genotype-guided tacrolimus dosing algorithm.

A map of copy number variations in the Tunisian population: a valuable tool for medical genomics in North Africa

Copy number variation (CNV) is considered as the most frequent type of structural variation in the human genome. Some CNVs can act on human phenotype diversity, encompassing rare Mendelian diseases and genomic disorders. The North African populations remain underrepresented in public genetic databases in terms of single-nucleotide variants as well as for larger genomic mutations. In this study, we present the first CNV map for a North African population using the Affymetrix Genome-Wide SNP (single-nucleotide polymorphism) array 6.0 array genotyping intensity data to call CNVs in 102 Tunisian healthy individuals. Two softwares, PennCNV and Birdsuite, were used to call CNVs in order to provide reliable data. Subsequent bioinformatic analyses were performed to explore their features and patterns. The CNV map of the Tunisian population includes 1083 CNVs spanning 61.443 Mb of the genome. The CNV length ranged from 1.017 kb to 2.074 Mb with an average of 56.734 kb. Deletions represent 57.43% of the identified CNVs, while duplications and the mixed loci are less represented. One hundred and three genes disrupted by CNVs are reported to cause 155 Mendelian diseases/phenotypes. Drug response genes were also reported to be affected by CNVs. Data on genes overlapped by deletions and duplications segments and the sequence properties in and around them also provided insights into the functional and health impacts of CNVs. These findings represent valuable clues to genetic diversity and personalized medicine in the Tunisian population as well as in the ethnically similar populations from North Africa.

New resources for genetic studies in maize (Zea mays L.): a genome-wide Maize6H-60K single nucleotide polymorphism array and its application.

Despite the availability of numerous molecular markers in maize, effective evaluation of all types of germplasm resources, accurate identification of varieties and analysis of a large number of materials in a timely, low-cost manner is challenging. Here, we present Maize6H-60K, a genome-wide single nucleotide polymorphism (SNP) array to facilitate maize genotyping. We first identified 160 million variants by sequencing data of 388 representative inbreds and then tiled 200000 high-quality variants on a screening array. These variants were further narrowed down to 61282 using stringent filtering criteria. Among the 60000 markers, 21460 SNPs (35%) were within genic regions and 12835 (21%) were located in coding regions. To assess their effectiveness, 329 inbreds, 221 hybrids, 34 parent-offspring sets and six breeding samples were genotyped. Overall, 48972 SNPs (80%) were categorized into the highest quality class, that of 'poly high resolution'. A total of 54658 (89.29%) and 53091 (86.73%) SNPs had minor allele frequency values≥0.20 in inbreds and hybrids respectively. A linkage disequilibrium (LD) analysis revealed that LD decline was in equilibrium when r2 was between 0.10 and 0.15, which corresponds to a physical distance of 400-600kb. UPGMA clustering analysis divided the 329 inbred lines into nine groups that were consistent with known pedigrees. A background analysis of breeding materials indicated that the 60000 markers were suitable for evaluation of breeding populations constructed by materials between or within heterotic groups. The developed Maize6H-60K array should be an important tool in maize genetic studies, variety identification and molecular breeding.

Do Polygenic Risk Scores For Cancer Susceptibility Associate With Risk Of Radiotherapy Toxicity?

Single nucleotide polymorphisms (SNPs) associated with increased susceptibility to cancer frequently lie in genes that might also modulate response to radiation. The purpose of this study is to evaluate whether individuals at increased genetic risk of developing cancer are also more likely to develop late radiotherapy-induced toxicities. We test the hypothesis that polygenic risk scores (PRS) for cancer susceptibility alter toxicity risk among cancer patients who received radiotherapy. Analysis included 1,134 breast, 3,521 prostate, and 610 lung cancer patients from radiotherapy cohorts from the Radiogenomics and REQUITE Consortia. All patients received radiotherapy alone or as part of combination treatment and were followed prospectively for development of toxicity in relevant tissues. Germline DNA was genotyped using a genome-wide SNP array with non-typed SNPs imputed using the 1000 Genomes reference data. A PRS was generated for each patient by summing risk alleles from cancer susceptibility SNPs identified in the literature - 352 for breast, 147 for prostate, 24 for lung cancer. A weighted PRS was similarly generated for prostate and lung cancer in which each SNP was first weighted by its odds ratio for cancer susceptibility; such a score was not available for breast cancer as the odds ratios vary by estrogen receptor status. Toxicity was quantified for each patient using STAT score, which is a previously validated measure of overall radiotherapy toxicity that combines multiple individual endpoints. Multivariable logistic regression tested association between PRS and toxicity STAT score (dichotomized at the mean plus one standard deviation) at 2 years after treatment for breast and prostate and up to 1 year for lung cancer patients, controlling for clinical covariates. Individual SNPs comprising the PRS were tested in a secondary analysis. No association was found between PRS and development of late radiotherapy toxicity among breast (PRS OR = 1.01, 95% CI = 1.00 to 1.02), prostate (PRS OR = 1.01, 95% CI = 1.00 to 1.03; weighted PRS OR = 1.10, 95%CI = 0.94 to 1.28) or lung cancer patients (PRS OR = 0.95, 95% CI = 0.88 to 1.02; weighted PRS OR = 0.77, 95% CI = 0.51 to 1.14). On multivariable analysis of individual SNPs, rs138944387 was associated with breast pain (beta = 1.12; 95% CI = 0.62 to 1.61; p = 1.09x10-5) and rs17513613 was associated with risk of breast edema (beta = -0.21; 95% CI = -0.31 to -0.12; p = 2.01x10-5). Cancer patients with a high polygenic predisposition to breast, prostate or lung cancer show no evidence of an increased risk of late radiotherapy toxicity. Thus, these patients can undergo standard treatment without an anticipated excess toxicity risk. The association between individual SNPs and late toxicity requires validation in independent cohorts and functional studies to elucidate the biologic mechanism underlying this shared risk.

Haplotype analysis of the internationally distributed BRCA1 c.3331_3334delCAAG founder mutation reveals a common ancestral origin in Iberia

BackgroundThe BRCA1 c.3331_3334delCAAG founder mutation has been reported in hereditary breast and ovarian cancer families from multiple Hispanic groups. We aimed to evaluate BRCA1 c.3331_3334delCAAG haplotype diversity in cases of European, African, and Latin American ancestry.MethodsBC mutation carrier cases from Colombia (n = 32), Spain (n = 13), Portugal (n = 2), Chile (n = 10), Africa (n = 1), and Brazil (n = 2) were genotyped with the genome-wide single nucleotide polymorphism (SNP) arrays to evaluate haplotype diversity around BRCA1 c.3331_3334delCAAG. Additional Portuguese (n = 13) and Brazilian (n = 18) BC mutation carriers were genotyped for 15 informative SNPs surrounding BRCA1. Data were phased using SHAPEIT2, and identical by descent regions were determined using BEAGLE and GERMLINE. DMLE+ was used to date the mutation in Colombia and Iberia.ResultsThe haplotype reconstruction revealed a shared 264.4-kb region among carriers from all six countries. The estimated mutation age was ~ 100 generations in Iberia and that it was introduced to South America early during the European colonization period.ConclusionsOur results suggest that this mutation originated in Iberia and later introduced to Colombia and South America at the time of Spanish colonization during the early 1500s. We also found that the Colombian mutation carriers had higher European ancestry, at the BRCA1 gene harboring chromosome 17, than controls, which further supported the European origin of the mutation. Understanding founder mutations in diverse populations has implications in implementing cost-effective, ancestry-informed screening.

Single nucleotide polymorphism array analysis of 102 patients with developmental delay and/or intellectual disability from Fujian, China

Developmental delay/intellectual disability (DD/ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In this study, we evaluated the usefulness of single nucleotide polymorphism (SNP) array in the detection of genetic causes of 102 DD/ID patients from Fujian (China). Of them, clinically relevant variants (including pathogenic and likely pathogenic), variants of uncertain significance (VOUS), and no clinically relevant variants (including likely benign and benign) were detected in 19, 4 and 79 patients, accounting for 18.6%, 3.9% and 77.5%, respectively, with a diagnostic yield of 18.6% in our study. Furthermore, we divided 19 clinically relevant variants into 4 groups, including chromosome aneuploidy (n = 1); large copy number variants (CNVs) (>10 Mb) (n = 8); known genomic disorders (n = 8), and likely pathogenic CNVs (n = 2). Moreover, we discussed our findings with respect to 4 cases of VOUS. Overall, we confirmed that DD/ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide SNP array in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with causal chromosomal aberrations, and discussed the potential implication in DD/ID of genes located within those CNVs or regions of homozygosity.

Extreme Phenotype Approach Suggests Taste Transduction Pathway for Carotid Plaque in a Multi-Ethnic Cohort.

Carotid plaque is a heritable trait and a strong predictor of vascular events. Several loci have been identified for carotid plaque, however, studies in minority populations are lacking. Within a multi-ethnic cohort, we have identified individuals with extreme total carotid plaque area (TCPA), that is, higher or lower TCPA than expected based on traditional vascular risk factors (age, sex, smoking, diabetes mellitus, hypertension, etc). We hypothesized that these individuals are enriched with genetic variants accounting for the plaque burden that cannot be explained by traditional vascular risk factors. Herein, we sought to identify the genetic basis for TCPA using the multi-ethnic cohort. Three hundred forty participants (170 from each extreme group) from 3 race/ethnic groups (53% Hispanic, 29% non-Hispanic Black, and 18% non-Hispanic White) were genotyped using a genome-wide single-nucleotide polymorphism (SNP) array and imputed using 1000Genome data. SNP-based analyses using logistic regression and gene-based analyses using VEGAS2 were performed within each race/ethnic group and then meta-analyzed. Genes with P<0.001 were included in an overrepresentation enrichment pathway analysis using WebGestalt. Promising findings were tested for association with ischemic stroke using the MEGASTROKE Consortium data set. No SNP or gene reached genome-wide significance. In the pathway analysis, GO:0050913 (sensory perception of bitter taste) gene set was significantly enriched (P=4.5×10-6, false discovery rate=0.04), which was confirmed in MEGASTROKE (P=0.01). Within the GO:0050913 gene set, 3 genes were associated with extreme TCPA in our study (P<0.001): TAS2R20, TAS2R50, and ITPR3. In TAS2R50, rs1376251 is the top SNP and has been associated with myocardial infarction by others. In ITPR3, a SNP with high regulatory potential (rs3818527, RegulomeScore=1f), and ITPR3 itself were among the top SNP-based and gene-based results and showed consistent evidence for association in all ethnic groups (P<0.05). Extreme TCPA analysis identified new candidate genes for carotid plaque in understudied populations.

Genome-wide non-HLA donor-recipient genetic differences influence renal allograft survival via early allograft fibrosis

Donor-recipient (D-R) differences at human leukocyte antigen (HLA) loci are currently incorporated into organ sharing, allocation and immunosuppression decisions. However, while acute rejection episodes have substantially diminished, progressive histologic damage occurs in allografts and improved long-term survival remains an unrealized goal among kidney recipients. Here we tested the hypothesis that non-HLA dependent, genome-wide D-R genetic differences could contribute to unchecked alloimmunity with histologic and functional consequences, culminating in long-term allograft failure. Genome-wide single nucleotide polymorphism (SNP) array data, excluding the HLA region, was utilized from 385 transplants to study the role of D-R differences upon serial histology and allograft survival. ADMIXTURE analysis was performed to quantitatively estimate ancestry in each D-R pair and PLINK was used to estimate the proportion of genome-shared identity-by-descent (pIBD) between D-R pairs. Subsequently, quantitative measures of recipient ancestry based on non-HLA SNPs was associated with death-censored allograft survival in adjusted Cox models. In D-R pairs of similar ancestry, pIBD was significantly associated with allograft survival independent of HLA mismatches in 224 transplants. Surprisingly, pIBD and recipient ancestry were not associated with clinical or subclinical rejection at any time post-transplant. Significantly, in multivariable analysis, pIBD inversely correlated with vascular intimal fibrosis in 160 biopsies obtained less than one year which in turn was significantly associated with allograft survival. Thus, our novel data show that non-HLA D-R differences associate with early vascular intimal fibrosis and allograft survival.

Genome Wide Association Study (GWAS) of cognitive impairment after blood or marrow transplantation (BMT) for hematologic malignancy.

1536 Background: Cognitive impairment is prevalent in hematologic malignancy patients treated with BMT (autologous: 18.7%; allogeneic: 35.7%; Sharafeldin JCO; 2018). Given the inter-individual variability in risk of cognitive impairment in this population, we investigated the role of genetic susceptibility using a genome-wide single nucleotide polymorphism (SNP) array platform to identify novel genetic associations. Methods: Discovery: Cognitive function was assessed objectively in 239 adult BMT recipients at pre-specified timepoints: pre-BMT and at 6 mo, 1y, 2y, and 3y post-BMT. A global deficit score (GDS - a summary score of 14 standardized neuropsychological tests) was computed for each patient; a higher score indicated greater cognitive impairment. SNPs passing standard quality control filters ( &gt; 1.4M) were used for analysis. Linear mixed effects models used GDS as the outcome, adjusted for age, sex, BMT type, baseline cognitive reserve, and the first four principal components. We used additive, codominant, and genotype models and an adjusted genome-wide significance threshold of 1.25 x 10−8. Replication: An independent cohort of 544 BMT survivors (192 cases with self-endorsed cognitive problems and 352 controls without) was used for replication. Results: Discovery: Median age at BMT was 51.3y; primary diagnoses: 47% leukemia, 32% lymphoma, 21% multiple myeloma; 57% males; 69% non-Hispanic whites: 50% allogeneic BMT, median GDS score = 0.22 (range 0-2). Forty-four SNPs were significantly associated with increased GDS (additive model: 3 SNPs; codominant model: 20 SNPs; genotype model: 21 SNPs). Estimates ranged from increase in GDS score by 0.28 points for each additional copy of risk allele, p = 1.07 x 10−8 to increase in GDS score by 1.82 points for two copies of risk allele, p = 2.3 x 10−11. Replication: Median age at BMT was 44y; primary diagnoses: 32% leukemia, 49% lymphoma, 19% multiple myeloma; 54% males; 80% non-Hispanic whites: 34% allogeneic BMT. Three SNPs were successfully replicated: rs116334183 resides within lncRNA-SEMA6D-2, which facilitates neuronal migration; rs13286152 86kb downstream of TLE-1, which promotes neuronal survival; and rs12486041 0.36Mb downstream from lncRNA-SPTSSB-1, which regulates sphingolipid production in neuronal axons and 0.36Mb upstream from TOMM22P6 linked to neural repair. Conclusions: In this first GWAS of cognitive impairment post-BMT, we identify 3 SNPs with plausible links to genes implicated in neuronal integrity. Functional studies are currently underway.

The place of metropolitan France in the European genomic landscape.

Unlike other European countries, the human population genetics and demographic history of Metropolitan France is surprisingly understudied. In this work, we combined newly genotyped samples from various zones in France with publicly available data and applied both allele frequency and haplotype-based methods to describe the internal structure of this country, using genome-wide single nucleotide polymorphism (SNP) array genotypes. We found out that French Basques, already known for their linguistic uniqueness, are genetically distinct from all other groups and that the populations from southwest France (namely the Gascony region) share a large proportion of their ancestry with Basques. Otherwise, the genetic makeup of the French population is relatively homogeneous and mostly related to Southern and Central European groups. However, a fine-grained, haplotype-based analysis revealed that Bretons slightly separated from the rest of the groups, due mostly to gene flow from the British Isles in a time frame that coincides both historically attested Celtic population movements to this area between the 3th and the ninth centuries CE, but also with a more ancient genetic continuity between Brittany and the British Isles related to the shared drift with hunter-gatherer populations. Haplotype-based methods also unveiled subtle internal structures and connections with the surrounding modern populations, particularly in the periphery of the country.

HLA class I alleles are associated with clinic-based migraine and increased risks of chronic migraine and medication overuse.

We aimed to evaluate associations of human leukocyte antigen variants with migraine or headache in hospital and population-based settings. The case-control study population, aged 30-70, included 605 clinic-based migraine patients in a medical center and 8449 population-based participants in Taiwan Biobank (TWB). Clinic-based cases were ascertained by neurologists. Participants in Taiwan Biobank were interviewed by a structured questionnaire including headache and migraine history; among them, 2394 had headache or migraine history while 6055 were free of headache and served as controls. All subjects were genotyped by Axiom Genome-Wide Single Nucleotide Polymorphism Arrays and imputed for eight classical human leukocyte antigen genes. Human leukocyte antigen frequencies were compared between clinic-based and self-reported patients and controls. We utilized likelihood ratio tests to examine human leukocyte antigen-disease associations and logistic regressions to estimate the effect of human leukocyte antigen alleles on migraine. Human leukocyte antigen-B and C showed significant associations with clinic-based migraine (q-value < 0.05). Human leukocyte antigen-B*39:01, human leukocyte antigen-B*51:01, human leukocyte antigen-B*58:01 and human leukocyte antigen-C*03:02 were significantly associated with migraine, with age and sex-adjusted odds ratios (95% CIs) of 1.80 (1.28-2.53), 1.50 (1.15-1.97), 1.36 (1.14-1.62) and 1.36 (1.14-1.62), correspondingly. Clinic-based migraineurs carrying human leukocyte antigen-B*58:01 or human leukocyte antigen-C*03:02 had 1.63 (1.11-2.39) -fold likelihood to have chronic migraine with medication-overuse headache compared to episodic migraine. However, no human leukocyte antigen genes were associated with self-reported headache or migraine in the community. Human leukocyte antigen class I genetic variants are positively associated with risk of clinic-based migraine but not self-reported migraine or headache and may contribute to migraine chronification and medication overuse.

Clonal relationship of synchronous head and neck cancer and esophageal cancer assessed by single nucleotide polymorphism-based loss of heterozygosity analysis

BackgroundThe prognoses of head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC) are poor, especially when both tumors occur at the same time. We examined the clonal relatedness of HNSCCs with synchronous ESCCs to confirm whether the second tumors were metastasis or separate second primary malignancies (SPMs) using loss of heterozygosity (LOH) analysis.MethodsTwenty-one pairs of formalin-fixed paraffin-embedded tissue from HNSCC patients with synchronous esophageal cancer were analyzed by single nucleotide polymorphism (SNP) array using the Illumina HumanCytoSNP FFPE-12 BeadChip (San Diego, CA), which contains approximately 300,000 probes. LOH was identified using Nexus Copy Number software (El Segundo, CA).ResultsComparing the LOH pattern between HNSCC and paired ESCC, we found that 20 out of 21 paired tissues had a high number of discordant LOHs (LOH identified solely in the primary HNSCC but not in synchronous ESCC at the same genomic location) and a low number of concordant LOHs (LOH at the same genomic location in both HNSCC and ESCC). Only one case fell into the undetermined category. Therefore, these 20 ESCCs were classified as SPMs or second field tumors (SFTs). Moreover, the HNSCC patients with molecularly confirmed esophageal SPM had significantly poorer survival than the other patients.ConclusionsWe propose the use of a genome-wide SNP array as a tool to differentiate metastatic tumors from SPM/SFT. The SNP array offers genome-wide LOH information that earlier microsatellite analysis studies lack. The ability to accurately identify SPM should contribute to a better treatment plan and follow-up care of these patients.

The Swedish Twin Registry: Content and Management as a Research Infrastructure.

The Swedish Twin Registry functions as research infrastructure containing information on 216,258 twins born between 1886 and 2015, of whom 86,199 pairs have zygosity determined by DNA, an intrapair similarity algorithm, or being of opposite sex. In essence, practically all twins alive and currently 9 years or older have been invited for participation and donation of DNA on which genomewide single nucleotide polymorphisms array genotyping has been performed. Content, management and alternatives for future improvements are discussed.

Genomic Patterns of Homozygosity in Chinese Local Cattle

Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5–1 Mb, Medium 1–5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.

De Novo and Therapy-Related Acute Myeloid Leukemia and Myelodysplastic Syndrome: Similarities and Differences in SNP-Array Detected Chromosomal Aberrations in Pre-Transplant Blood Samples

De Novo and Therapy-Related Acute Myeloid Leukemia and Myelodysplastic Syndrome: Similarities and Differences in SNP-Array Detected Chromosomal Aberrations in Pre-Transplant Blood Samples

Genome-wide association studies of structural birth defects: A review and commentary.

While there is strong evidence that genetic risk factors play an important role in the etiologies of structural birth defects, compared to other diseases, there have been relatively few genome-wide association studies (GWAS) of these conditions. We reviewed the current landscape of GWAS conducted for birth defects, noting novel insights, and future directions. This article reviews the literature with regard to GWAS of structural birth defects. Key defects included in this review include oral clefts, congenital heart defects (CHDs), biliary atresia, pyloric stenosis, hypospadias, craniosynostosis, and clubfoot. Additionally, other issues related to GWAS are considered, including the assessment of polygenic risk scores and issues related to genetic ancestry, as well as utilizing genome-wide single nucleotide polymorphism array data to evaluate gene-environment interactions and Mendelian randomization. For some birth defects, including oral clefts and CHDs, several novel susceptibility loci have been identified and replicated through GWAS, including 8q24 for oral clefts, DGKK for hypospadias, and 4p16 for CHDs. Relatively common birth defects for which there are currently no published GWAS include neural tube defects, anotia/microtia, anophthalmia/microphthalmia, gastroschisis, and omphalocele. Overall, GWAS have been successful in identifying several novel susceptibility genes and genomic regions for structural birth defects. These findings have provided new insights into the etiologies of these phenotypes. However, GWAS have been underutilized for understanding the genetic etiologies of several birth defects.

AMPK subunits harbor largely non-overlapping genetic determinants for body fat mass, glucose- and cholesterol metabolism

Abstract Context AMP-activated protein kinase (AMPK) is a heterotrimeric enzyme and central regulator of cellular energy metabolism. The impact of single nucleotide polymorphisms (SNPs) in all seven subunit genes on adiposity, glucose- and lipid metabolism has not been systematically studied yet. Objective To analyze the associations of common SNPs in all AMPK genes, and of different scores thereof, with adiposity, insulin sensitivity, insulin secretion, blood glucose, total-, LDL- and HDL-cholesterol and triglycerides. Study Design and Methods A cohort of 2789 non-diabetic subjects from the Tübingen Family study of type-2 diabetes, metabolically characterized by oral glucose tolerance test and genotyped by genome-wide SNP array was analyzed. Results We identified largely non-overlapping SNP sets across four AMPK genes (PRKAA1, PRKAA2, PRKAG2, PRKAG3) associated with adiposity, insulin sensitivity, insulin secretion, blood glucose, total-/LDL-cholesterol or HDL-cholesterol, respectively. A genetic score of body-fat-increasing alleles revealed per-allele effect sizes on BMI of +0.22 kg/m² (p=2.3·10-7), insulin sensitivity of -0.12·1019 L²/mol² (p=9.9·10-6) and 2-h blood glucose of +0.02 mmol/L (p=0.0048). Similar effects on blood glucose were observed with scores of insulin-sensitivity-reducing, insulin-secretion-reducing and glucose-raising alleles, respectively. A genetic cholesterol score increased total- and LDL-cholesterol by 1.17 mg/dL per allele (p=0.0002 and p=3.2·10-5, respectively), and a genetic HDL score decreased HDL-cholesterol by 0.32 mg/dL per allele (p=9.1·10-6). Conclusions We describe largely non-overlapping genetic determinants in AMPK genes for diabetes-/atherosclerosis-related traits which reflect the metabolic pathways controlled by the enzyme. Formation of trait-specific genetic scores revealed additivity of allele effects, with body-fat-raising alleles reaching a marked effect size.

AMPK Subunits Harbor Largely Nonoverlapping Genetic Determinants for Body Fat Mass, Glucose Metabolism, and Cholesterol Metabolism.

Adenosine monophosphate (AMP)-activated protein kinase (AMPK) is a heterotrimeric enzyme and central regulator of cellular energy metabolism. The impact of single nucleotide polymorphisms (SNPs) in all 7 AMPK subunit genes on adiposity, glucose metabolism, and lipid metabolism has not yet been systematically studied. To analyze the associations of common SNPs in all AMPK genes, and of different scores thereof, with adiposity, insulin sensitivity, insulin secretion, blood glucose, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, total cholesterol, and triglycerides. A cohort of 2789 nondiabetic participants from the Tübingen Family study of type 2 diabetes, metabolically characterized by oral glucose tolerance test and genotyped by genome-wide SNP array, was analyzed. We identified 6 largely nonoverlapping SNP sets across 4 AMPK genes (PRKAA1, PRKAA2, PRKAG2, PRKAG3) associated with adiposity, insulin sensitivity, insulin secretion, blood glucose, total/LDL cholesterol, or HDL cholesterol, respectively. A genetic score of body-fat-increasing alleles revealed per-allele effect sizes on body mass index (BMI) of +0.22 kg/m2 (P = 2.3 × 10-7), insulin sensitivity of -0.12 × 1019 L2/mol2 (P = 9.9 × 10-6) and 2-hour blood glucose of +0.02 mmol/L (P = 0.0048). Similar effects on blood glucose were observed with scores of insulin-sensitivity-reducing, insulin-secretion-reducing and glucose-raising alleles, respectively. A genetic cholesterol score increased total and LDL cholesterol by 1.17 mg/dL per allele (P = 0.0002 and P = 3.2 × 10-5, respectively), and a genetic HDL score decreased HDL cholesterol by 0.32 mg/dL per allele (P = 9.1 × 10-6). We describe largely nonoverlapping genetic determinants in AMPK genes for diabetes-/atherosclerosis-related traits, which reflect the metabolic pathways controlled by the enzyme. Formation of trait-specific genetic scores revealed additivity of allele effects, with body-fat-raising alleles reaching a marked effect size. (J Clin Endocrinol Metab XX: 0-0, 2019).

Genome-wide single nucleotide polymorphism array analysis unveils the origin of heterozygous androgenetic complete moles

Hydatidiform moles are abnormal pregnancies, which show trophoblastic hyperplasia. Most often, the nuclear genome in complete hydatidiform moles (CHMs) is composed of only paternal chromosomes. Diploid androgenetic conceptuses can be divided into homozygous and heterozygous CHMs. Heterozygous CHMs originate from two sperms or a diploid sperm, the distinction of which has not been established. Here, we assessed the origin of heterozygous CHMs using single nucleotide polymorphism (SNP) array. Thirteen heterozygous CHMs were analysed using B allele frequency (BAF) plotting to determine the centromeric zygosity status of all chromosomes. One case was from the duplication of a single sperm with an XY chromosome. In the other twelve cases, centromeric zygosity was random, i.e. mixed status. Thus, the twelve heterozygous CHMs were considered to be of dispermic origin but not diploid sperm origin. BAF plotting of SNP array can be a powerful tool to estimate the type of hydatidiform moles.