Genome-wide SNP Array Research Articles

Prognostic value of myocardial redox signalling: a machine learning multi-omics approach

Abstract Background Oxidative stress has been proposed to be implicated in cardiovascular pathology. Studies have linked myocardial oxidative stress with the development of atrial fibrillation, but its role in the prediction of long-term outcomes and mortality is yet to be elucidated. Purpose To apply discovery network transcriptomics and genomics to atrial tissue (AT) obtained from patients undergoing cardiac surgery, to phenotype myocardial redox-state and identify potential therapeutic targets. Methods We included 1,032 patients undergoing cardiac surgery. Arm 1 included 258 patients in whom atrial tissue (right atrial appendage) was used for ex-vivo quantification of NOX-derived superoxide by lucigenin-enhanced chemiluminescence. Arm 2 included 414 patients in whom exploratory, unsupervised gene network analysis in human atrial tissue RNA sequencing data was performed to identify atrial tissue redox-sensitive signatures (blue signature). Arm 3 included 881 patients genotyped with the genome-wide SNP array UK Biobank Axiom Array and used for machine learning construction of GenRedOx, a SNP model built to predict the blue transcriptomic signature. Associations with future incidence of major adverse myocardial events (MAME: cardiovascular death and/or heart failure) was assessed across all arms using cox regression models (adjusted for age, sex, hypertension, dyslipidaemia, diabetes mellitus, body mass index, and plasma TNFa). Results Over a median follow-up of 5.27 years [IQR: 4.29-6.83] high atrial tissue (AT) NOX-derived superoxide was independently associated with MAME risk (Adj. HR[95%CI]: 11.7 [2.18 , 62.82], p=0.004, a). Unsupervised transcriptomic analysis in Arm 2 revealed 15 coexpressed gene ‘modules’ or 'signatures' (b). The blue signature was significantly associated with AT superoxide production with "immune response-regulating and activating signalling" being amongst the top enriched pathways. Patients with high eigengene values for the blue signature showed a 5.5-fold higher adjusted risk of MAME (c). In Arm 3, extreme gradient boosting of SNP data, trained using the blue transcriptomic signature as ground truth, revealed GenRedOx (d), a genomic artificial intelligence score, which was found to be prognostic of MAME in the validation stage (e). Homozygosity for the minor allele of SNP rs723897 in the Chemokine-Like Factor Super Family 7 (CMTM7) gene had the highest gain in the model. Conclusion We present for the first time two novel human myocardial transcriptomic and genomic signatures that reflect changes in redox state and identify long-term cardiovascular risk. Targeting pathways in the myocardium related with immune response signalling may lead to the development of novel therapeutics in cardiovascular disease.

Comprehensive Analyses of Somatic Copy Number Alterations and Mutations Based on the Adenoma-Carcinoma Sequence.

Identifying molecular alterations in the adenoma and carcinoma components within the same tumor would greatly contribute to understanding the neoplastic progression of early colorectal cancer. We examined somatic copy number alterations (SCNAs) and mutations involved in the adenoma and carcinoma components obtained from the same tumor in 46 cases of microsatellite-stable carcinoma in adenoma, using a genome-wide SNP array and gene mutation panel. In addition, we also performed hierarchical clustering to determine the SCNA frequencies in the tumors, resulting in stratification of the samples into two subgroups according to SCNA frequency. Subgroup 1 was characterized by multiple SCNAs and carcinoma components exclusively, while Subgroup 2 was characterized by a low frequency of SCNAs and both the adenoma and carcinoma components. The numbers of total genes and genes with gains were higher in the carcinoma than adenoma components. The three most frequent gains in both components were located at 1p36.33-1q44, 2p25.3-2q37.3, and 3p26.3-3q29. However, no candidate genes mapped to these regions. APC and KRAS mutations were common in both components, whereas the frequency of TP53 mutations was statistically higher in the carcinoma than adenoma component. However, TP53 mutations were not correlated with SCNA frequency. We suggest that considerable SCNAs and TP53 mutations are required for progression from adenoma to carcinoma within the same intramucosal neoplastic lesion.

The genetic landscape of autism spectrum disorder in the Middle Eastern population.

Introduction: Autism spectrum disorder (ASD) is characterized by aberrations in social interaction and communication associated with repetitive behaviors and interests, with strong clinical heterogeneity. Genetic factors play an important role in ASD, but about 75% of ASD cases have an undetermined genetic risk. Methods: We extensively investigated an ASD cohort made of 102 families from the Middle Eastern population of Qatar. First, we investigated the copy number variations (CNV) contribution using genome-wide SNP arrays. Next, we employed Next Generation Sequencing (NGS) to identify de novo or inherited variants contributing to the ASD etiology and its associated comorbid conditions in families with complete trios (affected child and the parents). Results: Our analysis revealed 16 CNV regions located in genomic regions implicated in ASD. The analysis of the 88 ASD cases identified 41 genes in 39 ASD subjects with de novo (n = 24) or inherited variants (n = 22). We identified three novel de novo variants in new candidate genes for ASD (DTX4, ARMC6, and B3GNT3). Also, we have identified 15 de novo variants in genes that were previously implicated in ASD or related neurodevelopmental disorders (PHF21A, WASF1, TCF20, DEAF1, MED13, CREBBP, KDM6B, SMURF1, ADNP, CACNA1G, MYT1L, KIF13B, GRIA2, CHM, and KCNK9). Additionally, we defined eight novel recessive variants (RYR2, DNAH3, TSPYL2, UPF3B KDM5C, LYST, and WNK3), four of which were X-linked. Conclusion: Despite the ASD multifactorial etiology that hinders ASD genetic risk discovery, the number of identified novel or known putative ASD genetic variants was appreciable. Nevertheless, this study represents the first comprehensive characterization of ASD genetic risk in Qatar's Middle Eastern population.

High-resolution genomic profiling and locus-specific FISH in subcutaneous and visceral adipose tissue of obese patients.

Obesity is known as a heterogeneous and multifactorial disease. The distribution of body fat is crucial for the development of metabolic complications. Comprehensive genetic analyses on different fat tissues are rare but necessary to provide more detailed information. Therefore, we performed genetic analyses of three patients with obesity using high resolution genome wide SNP array (blood, visceral fat tissue) and fluorescence in situ hybridization (FISH) analyses (visceral and subcutaneous fat tissue). Altogether, we identified 31 small Copy Number Variations (losses: 1p31.1, 1p22.2, 1q21.3, 2q34, 2q37.1, 3q28, 6p25.3, 7q31.33, 7q33, 8p23.3, 10q22.3, 11p15.4, 11p15.1, 11p14.2, 11p12, 13q12.3, 15q11.2-q13.1, 15q13.3, 20q13.2, 22q11.21; gains: 2q22.1-q22.2, 3p14.3, 4p16.3, 4q32.2, 6q27, 7p14.3, 7q34, 11p12, 12p11.21, 16p11.2-p11.1, 17q21.31) and 289 small copy-neutral Loss of Heterozygosity (cn-LOH). For the chromosomal region 15q11.2-q13.1, we detected a microdeletion (Prader-Willi-Syndrome) in one patient. Interestingly, we identified chromosomal SNP differences between EDTA-blood and visceral fat tissue (deletion and gain). Small losses of 7q31.33, 7q33, 11p14.2, 11p12, 13q12.3 as well as small gain of 7q34 were detected only in fat tissue and not in blood. Furthermore, FISH analyses on 7q31.33, 7q33 and 11p12 revealed differences between subcutaneous and visceral fat tissue. Generally, the deletions were detected more frequent in visceral fat tissue. Predominantly detected cn-LOH vs. CNV suggests a meaning of these cn-LOH for the pathogenesis of obesity. We conclude that the SNP array and FISH analyses used is applicable to generate more information for basic research on difficult cell subpopulations (e.g., visceral adipose tissue) and could opens up new diagnostic aspects in the field of obesity. Altogether, the significance of these mostly not yet described genetic aberrations in different fat tissues needs to confirmed in a larger series.

The use of high-resolution SNP arrays to detect congenital cardiac defects

Objective Copy number variations (CNVs) detected by high-resolution single nucleotide polymorphism microarrays (SNP arrays) have been associated with congenital heart defects (CHDs). The genetic mechanism underlying the development of CHDs remains unclear. Methods High-resolution SNP arrays were used to detect CNVs and traditional chromosomal analyses, respectively, were carried out on 60 and 249 fetuses from gestational 12–37 weeks old, having isolated or complex CHDs that were diagnosed using prenatal ultrasound. Results Twenty of the 60 fetuses (33.5%) had abnormalities, of which 23 CNVs (12 pathogenic, five probable pathogenic and six of undetermined significance) were detected by SNP arrays, and two distinct CNVs were present in three of these fetuses. In addition, in 39 patients with isolated congenital heart disease who had normal karyotypes, abnormal CNVs were present in 28.2% (11/39), and in patients with complex coronary artery disease, 19.0% (4/21) had abnormal karyotypes and 42.9% (9/21) had abnormal CNVs. In patients with complex coronary artery disease, 19.0% (4/21) had abnormal karyotypes and 42.9% (9/21) had abnormal CNVs. Conclusions In conclusion, genome-wide high-resolution SNP array can improve the diagnostic rate and uncover additional pathogenic CNVs. The submicroscopic deletions and duplications of Online Mendelian Inheritance in Man (OMIM) genes found in this study have haploinsufficient (deletion) or triplosensitive (duplication) traits, which further clarify the etiology and inheritance of CHDs.

The collective effects of genetic variants and complex traits.

Traditional approaches in studying the genetics of complex traits have focused on identifying specific genetic variants. However, the collective effects of variants have remained largely unexplored. Here, we evaluated whether traits could be influenced by the collective effects of variants across the entire protein coding-region of the genome or the entire genome. We studied the UK Biobank exome sequencing data of 167,246 individuals as well as the genome-wide SNP array data of 408,868 individuals. We calculated for each individual four different measures of genetic variation such as heterozygosity and number of variants and two different measures of the overall deleteriousness of all variants, and performed correlations with 17 representative traits that have been studied previously. Linear regression analysis was performed with adjustment for age, sex, and genetic principal components. The results showed a high correlation among the six different measures and an inverse association of two well-correlated traits (educational attainment and height) with the total number of all variants as well as the overall deleteriousness of all variants. We have also categorized the genes based on whether they are expressed in the brain and found that the association with educational attainment only held for the brain-expressed genes. No other traits examined showed a significant correlation with the brain-expressed genes. The study demonstrates that common traits could be studied by analyzing the overall genetic variation and suggests that educational attainment is inversely related to genetic variation.

Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population

BackgroundPharmacogenomics (PGx) aims to utilize a patient’s genetic data to enable safer and more effective prescribing of medications. The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides guidelines with strong evidence for 24 genes that affect 72 medications. Despite strong evidence linking PGx alleles to drug response, there is a large gap in the implementation and return of actionable pharmacogenetic findings to patients in standard clinical practice. In this study, we evaluated opportunities for genetically guided medication prescribing in a diverse health system and determined the frequencies of actionable PGx alleles in an ancestrally diverse biobank population.MethodsA retrospective analysis of the Penn Medicine electronic health records (EHRs), which includes ~ 3.3 million patients between 2012 and 2020, provides a snapshot of the trends in prescriptions for drugs with genotype-based prescribing guidelines (‘CPIC level A or B’) in the Penn Medicine health system. The Penn Medicine BioBank (PMBB) consists of a diverse group of 43,359 participants whose EHRs are linked to genome-wide SNP array and whole exome sequencing (WES) data. We used the Pharmacogenomics Clinical Annotation Tool (PharmCAT), to annotate PGx alleles from PMBB variant call format (VCF) files and identify samples with actionable PGx alleles.ResultsWe identified ~ 316.000 unique patients that were prescribed at least 2 drugs with CPIC Level A or B guidelines. Genetic analysis in PMBB identified that 98.9% of participants carry one or more PGx actionable alleles where treatment modification would be recommended. After linking the genetic data with prescription data from the EHR, 14.2% of participants (n = 6157) were prescribed medications that could be impacted by their genotype (as indicated by their PharmCAT report). For example, 856 participants received clopidogrel who carried CYP2C19 reduced function alleles, placing them at increased risk for major adverse cardiovascular events. When we stratified by genetic ancestry, we found disparities in PGx allele frequencies and clinical burden. Clopidogrel users of Asian ancestry in PMBB had significantly higher rates of CYP2C19 actionable alleles than European ancestry users of clopidrogrel (p < 0.0001, OR = 3.68).ConclusionsClinically actionable PGx alleles are highly prevalent in our health system and many patients were prescribed medications that could be affected by PGx alleles. These results illustrate the potential utility of preemptive genotyping for tailoring of medications and implementation of PGx into routine clinical care.

Exploring the relationships between genetic, linguistic and geographic distances in Bantu‐speaking populations

ObjectivesThe predominance of Bantu languages in sub‐Saharan Africa has sparked a large debate over the processes through which they came to disperse over time and space—the “Bantu expansion.” The overall genetic similarity shown by Bantu‐speaking populations indicates that movement of people occurred too, but the extent of the correlation between genetics, linguistics and geography has been a matter of debate among scholars of different disciplines. In this work, we aim to investigate how genetic, linguistic and geographic distances relate to each other in Bantu‐speaking populations.MethodsWe analyzed genome‐wide SNP array data from a set of 37 Bantu and non‐Bantu‐speaking populations together with related linguistic and geographic data. Due to the complex demographic relationships resulting from events of admixture in the history of these populations, we develop and implement a method for controlling the signatures of admixture.ResultsGenetic distances were only minimally correlated with linguistic and geographic distances, possibly as the result of gene flow from neighboring groups into Bantu‐speaking populations. When signatures of admixture are controlled for, the correlation of genetic data with linguistic and geographic distances significantly increases.DiscussionThe increase of the correlation between linguistic and genetic distances after the signatures of admixture are taken into account is in agreement with a scenario of spatial co‐dispersal of languages and people. Additional specific cultural and demographic dynamics have probably further affected the relationship between language and genetics, which will be necessary to take into account when integrating multidisciplinary data to reconstruct the history of populations.

Hepatic Expression of the Na+-Taurocholate Cotransporting Polypeptide Is Independent from Genetic Variation.

The hepatic Na+-taurocholate cotransporting polypeptide NTCP/SLC10A1 is important for the uptake of bile salts and selected drugs. Its inhibition results in increased systemic bile salt concentrations. NTCP is also the entry receptor for the hepatitis B/D virus. We investigated interindividual hepatic SLC10A1/NTCP expression using various omics technologies. SLC10A1/NTCP mRNA expression/protein abundance was quantified in well-characterized 143 human livers by real-time PCR and LC-MS/MS-based targeted proteomics. Genome-wide SNP arrays and SLC10A1 next-generation sequencing were used for genomic analyses. SLC10A1 DNA methylation was assessed through MALDI-TOF MS. Transcriptomics and untargeted metabolomics (UHPLC-Q-TOF-MS) were correlated to identify NTCP-related metabolic pathways. SLC10A1 mRNA and NTCP protein levels varied 44-fold and 10.4-fold, respectively. Non-genetic factors (e.g., smoking, alcohol consumption) influenced significantly NTCP expression. Genetic variants in SLC10A1 or other genes do not explain expression variability which was validated in livers (n = 50) from The Cancer Genome Atlas. The identified two missense SLC10A1 variants did not impair transport function in transfectants. Specific CpG sites in SLC10A1 as well as single metabolic alterations and pathways (e.g., peroxisomal and bile acid synthesis) were significantly associated with expression. Inter-individual variability of NTCP expression is multifactorial with the contribution of clinical factors, DNA methylation, transcriptional regulation as well as hepatic metabolism, but not genetic variation.

A protocol for recruiting and analyzing the disease-oriented Russian disc degeneration study (RuDDS) biobank for functional omics studies of lumbar disc degeneration

Lumbar intervertebral disc degeneration (DD) disease is one of the main risk factors for low back pain and a leading cause of population absenteeism and disability worldwide. Despite a variety of biological studies, lumbar DD is not yet fully understood, partially because there are only few studies that use systematic and integrative approaches. This urges the need for studies that integrate different omics (including genomics and transcriptomics) measured on samples within a single cohort. This protocol describes a disease-oriented Russian disc degeneration study (RuDDS) biobank recruitment and analyses aimed to facilitate further omics studies of lumbar DD integrating genomic, transcriptomic and glycomic data. A total of 1,100 participants aged over 18 with available lumbar MRI scans, medical histories and biological material (whole blood, plasma and intervertebral disc tissue samples from surgically treated patients) will be enrolled during the three-year period from two Russian clinical centers. Whole blood, plasma and disc tissue specimens will be used for genotyping with genome-wide SNP-arrays, glycome profiling and RNA sequencing, respectively. Omics data will be further used for a genome-wide association study of lumbar DD with in silico functional annotation, analysis of plasma glycome and lumbar DD disease interactions and transcriptomic data analysis including an investigation of differential expression patterns associated with lumbar DD disease. Statistical tests applied in each of the analyses will meet the standard criteria specific to the attributed study field. In a long term, the results of the study will expand fundamental knowledge about lumbar DD development and contribute to the elaboration of novel personalized approaches for disease prediction and therapy. Additionally to the lumbar disc degeneration study, a RuDDS cohort could be used for other genetic studies, as it will have unique omics data. Trial registration number NCT04600544.

Analysis of HLA Variants and Graves' Disease and Its Comorbidities Using a High Resolution Imputation System to Examine Electronic Medical Health Records.

Hyperthyroidism is a prevalent endocrine disorder, and genetics play a major role in the development of thyroid-associated diseases. In particular, the inheritance of HLA has been demonstrated to induce the highest susceptibility to Graves’ disease (GD). However, thus far, no studies have reported the contribution of HLA to the development of GD and the complications that follow. Thus, in the present study, to the best of our knowledge, for the first time, a powerful imputation method, HIBAG, was used to predict the HLA subtypes among populations with available genome-wide SNP array data from the China Medical University Hospital (CMUH). The disease status was extracted from the CMUH electronic medical records; a total of 2,998 subjects with GD were identified as the cases to be tested and 29,083 subjects without any diagnosis of thyroid disorders were randomly selected as the controls. A total of 12 HLA class I genotypes (HLA-A*02:07-*11:01, HLA-B*40:01-*46:01 and *46:01-*46:01, and HLA-C*01:02-*01:02, *01:02-*03:04, and *01:02-*07:02) and 17 HLA class II genotypes (HLA-DPA1*02:02-*02:02, HLA-DPB1*02:01-*05:01, *02:02-*05:01, and *04:01-*05:01, HLA-DQA1*03:02, HLA-DRB1*09:01-*15:01, and *09:01-*09:01) were found to be associated with GD in the Taiwanese population. Moreover, the HLA subtypes HLA-A*11:01, HLA-B*46:01, HLA-DPA1*01:03, and HLA-DPB1*05:01 were found to be associated with heart disease, stroke, diabetes, and hypertension among subjects with GD. Our data suggest that several HLA alleles are markedly associated with GD and its comorbidities, including heart disease, hypertension, and diabetes.

EP170: When cfDNA screening deceives: A rare case of mosaicism for 46,XX/47,XXY with uniparental isodisomy and genital atypia

Sex chromosome aneuploidy (SCA) identified on cell free DNA screening (cfDNA) presents a challenge for both prenatal counseling, and care planning for the infant after delivery. It is well understood that post-natal evaluation must include chromosomal analysis to confirm SCAs and evaluate for mosaicism. This is traditionally achieved using karyotype, with or without FISH for Y-component. The findings are important for diagnosis care planning, including for individuals with Intersex/Differences of Sex Development (I/DSD) traits. In the case of I/DSD traits, recommendations of gender of rearing are complex and require consideration of multiple pieces of evidence that include, but are not limited to, chromosomes. Despite being a screening rather than a diagnostic test, the advent of cfDNA analysis has generated added prenatal information that can often color the complex medical and psychosocial thought process of assignment of gender of rearing in cases of ambiguity at birth. I/DSD traits are defined as atypical/non-binary development of chromosomal, gonadal and/or anatomic sex. SCAs are a frequent cause of DSD, most commonly mosaic monosomy X (“Turner cells”) with Y chromosome material. Mosaic SCAs involving 47,XXY (“Klinefelter cells”) is a rare cause of DSDs. Mosaicism involving 47,XXY is typically 46,XY/47,XXY, and is not associated with genital atypia. We present a case of a patient who was initially erroneously reported as 46, XX on cfDNA screening. Post-natal confirmation using genome-wide SNP array showed instead 46,XX/47,XXY mosaicism. Furthermore, both cell lines contained uniparental isodisomy of the entire chromosome X. The infant was evaluated at 6-months-old for non-binary genital (“ambiguity”) first noted at birth. Patient was naturally conceived, born to a G1P0-P1 mother, and with normal prenatal screening and ultrasounds by report. CfDNA screen report was low risk with 46,XX, and the infant was therefore assigned female at birth. Patient was SGA with non-dysmorphic facies, and external genitalia exam notable for: Prader 3 clitorophallus, with one identifiable opening on the ventral aspect, and fused, ruggated scrotolabial folds without palpable gonads. Labs at the time of mini-puberty of infancy (8 weeks of life) provided evidence of gonadal function, despite absence of gonads on imaging: testosterone (188 ng/dL, normal range for 46,XX <10 ng/dL; normal range for 46,XY 60-400 ng/dL); AMH (27.49 ng/mL, normal range for 46,XX 0.53-7.78 ng/mL); estradiol (1.9 pg/mL, normal range for 46,XX 5-50 pg/mL); and pubertal LH and FSH concentrations. This suggested the presence of functional testicular tissue. Karyotype and SNP microarray were completed. SNP initially reported this patient as mosaic for chromosomal complement 45,X/46,XY (arr[hg19] Yp11.32q12(10,814-59,339,753)x0 [75%]). However, karyotype results were then noted to be mosaic for 46, XX [25]/47, XXY [5], with further analysis showing the patient had total uniparental isodisomy of the entire X chromosome in 100% of her cells, with deletion of the entire Y as above in 75% of cells. Uniparental isodisomy of the entire X chromosome is exceedingly rare and is due to monosomy rescue in the case of a 45,X complement, or maternal nondisjunction and lack of paternal sex chromosome complement. It is most commonly reported in the literature in 46,XX female patients with X-linked conditions such as Duchene muscular dystrophy or Fragile X. Our patient showed no true 45,X complement on her microarray, which would be expected in the setting of monosomy rescue. Such a monosomy rescue mechanism is also difficult to reconcile with the presence of Y chromosome. Our hypothesis is that the initial zygote was 47,XXY with the UPD X due to maternal non-disjunction at meiosis II. The Y was later lost in one cell line. However, it is also atypical that her X shows no evidence of crossing over if this was in fact a meiosis II non-disjunction event. Her Y also must have been lost early on in development, as her placenta likely had predominantly 46, XX cells for her cfDNA screen results to show no Y component. Less than ten patients have been previously reported with mosaicism for 46,XX/47,XXY. Of note, the majority of these patients did not have genital differences at birth, and all were assigned male. This is despite well-documented cases in the literature that mosaicism of 45,X/46,XY is commonly associated with genital atypia. Patients with mosaicism for Y containing cells are often picked up as having a Y component on their cfDNA results, where sensitivity to determine presence of a Y chromosome is 99.4%. It is important to understand cfDNA analysis as a screening test, and not a diagnostic test like a karyotype or SNP microarray. Under some circumstances, chromosomal aneuploidies, including SCAs, can be missed. Therefore, regardless of cfDNA screen results, karyotype and SNP microarray are important tests to consider in the setting of a DSD where mosaicism for a Y-containing line is a common diagnosis.

Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer.

Evolutionary copy-number patterns may be associated with survival in patients with resected PDAC.

Evaluation of DNA Methylation at Birth in Monozygotic Twin Pairs Discordant for Acute Lymphoblastic Leukemia

Background: Aberrant patterns of DNA methylation constitute a key feature of pediatric acute lymphoblastic leukemia (ALL) at diagnosis, however its role as a predisposing or early contributor to the development of ALL remains unknown. We employed a discordant monozygotic twin model to identify epigenetic variation associated with future development of pediatric ALL through evaluation of DNA methylation at birth.Methods: Twin pairs discordant for the development of pediatric ALL were identified using linked data from the California Cancer Registry and California Birth Statistical Master File spanning from 1989 to 2015. Archived dried neonatal blood spots were obtained from 86 same-gender twin pairs with available materials from the California Biobank Program. Following isolation of genomic DNA from DBS samples, monozygosity was confirmed in 43 of 86 twin pairs through an identity-by-descent analysis from a genome-wide SNP-array. Epigenome-wide DNA methylation assessment of the 43 discordant monozygotic twin pairs was conducted using the Illumina Infinium MethylationEPIC BeadChip kit (Illumina, San Diego, CA, USA). Data preprocessing and quality control measures were conducted in R, using SeSAMe for data normalization. Two twin pairs were omitted due to failure to pass quality control measures. Within-pair analysis was conducted through identification of array probes with absolute differences in methylation beta values greater than 15% between case and control siblings of a twin pair unit. Differentially methylated probes (DMP) were identified using a conditional logistic regression model accounting for array-specific variation, nucleated cell proportions, and appropriate control for the paired nature of the dataset. Differentially methylated regions (DMR) were defined by regional correlation of p-values from the conditional logistic regression model. Gene set enrichment analysis was conducted on significant probes identified through the within pair and regression analysis.Results: The discordant twin cohort (n = 41 pairs) included 24 female and 17 male pairs. Median gestational age was 258 days, ranging from 184 to 306 days. Age of diagnosis in the case twin ranged from <1 to 23 years (median = 5). There was no significant association between birthweight and case status (paired Wilcoxon signed rank test p = 0.22). No significant differences in nucleated cell proportions were identified in deconvolution analysis. Within-pair analysis identified a total of 18,001 probes with absolute methylation variation greater than 15% across the 41 twin pairs, with 3,984 recurrently variable across more than one pair. Gene ontology analysis of these recurrently variable sites revealed an enrichment of immune-related processes in 7 of the top 15 terms with nominal p-value <0.05, though no terms were significant after correction for multiple comparisons. Conditional logistic regression was conducted on 37 twin pairs, with T-cell cases (n=4) omitted to improve data resolution. This resulted in 240 significant DMPs with p-values below an FDR threshold of 0.05. Of these significant probes, 20 associate with genes previously reported to have altered DNA methylation in ALL at diagnosis. Regional analysis identified 10 significant DMRs with adjusted p-values below 0.05, with the top association encompassing a 454bp region on chromosome 6 located near TRIM39-RPP21 (adjusted p-value 2.39e-05). Notably, conditional regression analysis revealed a significant negative bias in coefficients (409,812 of 710,010 probes, binomial exact test p <2.2e-16), indicating a global tendency toward hypomethylation in cases compared to unaffected siblings (Figure 1). The strength of this bias was greater in probes associated with open sea regions compared to those in island regions, as well as promoter-associated probes.Conclusions: This novel analysis of DNA methylation at birth in ALL-discordant monozygotic twins identified sites of differential methylation associated with immune regulation. In addition, these results provide evidence of an association between global DNA hypomethylation and future development of ALL in one member of a genetically identical twin pair. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

A Comprehensive Review on the Role of Genetic Factors in Neuromyelitis Optica Spectrum Disorder.

Neuromyelitis optica spectrum disorders (NMOSD) comprise a variety of disorders being described by optic neuritis and myelitis. This disorder is mostly observed in sporadic form, yet 3% of cases are familial NMO. Different series of familial NMO cases have been reported up to now, with some of them being associated with certain HLA haplotypes. Assessment of HLA allele and haplotypes has also revealed association between some alleles within HLA-DRB1 or other loci and sporadic NMO. More recently, genome-wide SNP arrays have shown some susceptibility loci for NMO. In the current manuscript, we review available information about the role of genetic factors in NMO.

The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

Pedigree information is of fundamental importance in breeding programs and related genetics efforts. However, many individuals have unknown pedigrees. While methods to identify and confirm direct parent–offspring relationships are routine, those for other types of close relationships have yet to be effectively and widely implemented with plants, due to complications such as asexual propagation and extensive inbreeding. The objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes (referred to in this study as “summed potential lengths of shared haplotypes”, SPLoSH). A custom Python script, HapShared, was developed to generate SPLoSH data in apple and sweet cherry. HapShared was used to establish empirical distributions of SPLoSH data for known relationships in these crops. These distributions were then used to estimate previously unknown relationships. Case studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH data. For cherry, a full-sib relationship was deduced for ‘Emperor Francis, and ‘Schmidt’, a half-sib relationship for ‘Van’ and ‘Windsor’, and the paternal grandparents of ‘Stella’ were confirmed. For apple, 29 cultivars were found to share an unknown parent, the pedigree of the unknown parent of ‘Cox’s Pomona’ was reconstructed, and ‘Fameuse’ was deduced to be a likely grandparent of ‘McIntosh’. Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets, integrated genetic maps, and previously identified pedigree relationships. Crops with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

The conserved ASTN2/BRINP1 locus at 9q33.1\u201333.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain

We investigated the genetic causes of major mental disorders (MMDs) including schizophrenia, bipolar disorder I, major depressive disorder and attention deficit hyperactive disorder, in a large family pedigree from Alpujarras, South of Spain, a region with high prevalence of psychotic disorders. We applied a systematic genomic approach based on karyotyping (n = 4), genotyping by genome-wide SNP array (n = 34) and whole-genome sequencing (n = 12). We performed genome-wide linkage analysis, family-based association analysis and polygenic risk score estimates. Significant linkage was obtained at chromosome 9 (9q33.1–33.2, LOD score = 4.11), a suggestive region that contains five candidate genes ASTN2, BRINP1, C5, TLR4 and TRIM32, previously associated with MMDs. Comprehensive analysis associated the MMD phenotype with genes of the immune system with dual brain functions. Moreover, the psychotic phenotype was enriched for genes involved in synapsis. These results should be considered once studying the genetics of psychiatric disorders in other families, especially the ones from the same region, since founder effects may be related to the high prevalence.

A genome-wide analysis of the molecular alterations occurring in the adenomatous and carcinomatous components of the same tumor based on the adenoma-carcinoma sequence.

Identification of molecular alterations occurring in the adenomatous and carcinomatous components within the same tumor would greatly enhance understanding of the neoplastic progression of colorectal cancer. We examined somatic copy number alterations (SCNAs) and mRNA expression at the corresponding loci involved in the adenoma–carcinoma sequence in the isolated adenomatous and cancer glands of the same tumor in 15 cases of microsatellite‐stable “carcinoma in adenoma,” using genome‐wide SNP and global gene expression arrays. Multiple copy‐neutral loss of heterozygosity events were detected at 4q13.2, 15q15.1, and 14q24.3 in the adenomatous component and at 4q13.2, 15q15.1, and 14q24.3 in the carcinomatous component. There were significant differences in the copy number (CN) gain frequencies at 20q11.21–q13.33, 8q13.3, 8p23.1, and 8q21.2–q22.2 between the adenomatous and carcinomatous components. Finally, we found a high frequency of five genotypes involving CN gain with upregulated expression of the corresponding gene (RPS21, MIR3654, RSP20, SNORD54, or ASPH) in the carcinomatous component, whereas none of these genotypes were detected in the adenomatous component. This finding is interesting in that CN gain with upregulated gene expression may enhance gene function and play a crucial role in the progression of an adenoma into a carcinomatous lesion.

Identification and characterization of GLOBE, a major gene controlling fruit shape and impacting fruit size and marketability in tomato

Within large-fruited germplasm, fruit size is influenced by flat and globe shapes. Whereas flat fruits are smaller and retain better marketability, globe fruits are larger and more prone to cuticle disorders. Commercial hybrids are often developed from crosses between flat and globe shaped parents because flat shape is thought to be dominant and fruit size intermediate. The objectives of this study were to determine the genetic basis of flat/globe fruit shape in large-fruited fresh-market tomato germplasm and to characterize its effects on several fruit traits. Twenty-three advanced single plant selections from the Fla. 8000 × Fla. 8111B cross were selectively genotyped using a genome-wide SNP array, and inclusive composite interval mapping identified a single locus on the upper arm of chromosome 12 associated with shape, which we termed globe. A 238-plant F2 population and 69 recombinant inbred lines for this region from the same parents delimited globe to approximately 392-kilobases. A germplasm survey representing materials from multiple breeding programs demonstrated that the locus explains the flat/globe shape broadly. A single base insertion in an exon of Solyc12g006860, a gene annotated as a brassinosteroid hydroxylase, segregated completely with shape in all populations tested. CRISPR/Cas9 knock out plants confirmed this gene as underlying the globe locus. In silico analysis of the mutant allele of GLOBE among 595 wild and domesticated accessions suggested that the allele arose very late in the domestication process. Fruit measurements in three genetic backgrounds evidenced that globe impacts fruit size and several fruit shape attributes, pedicel length/width, and susceptibility of fruit to weather check. The mutant allele of GLOBE appears mostly recessive for all traits except fruit size where it acts additively.

Comparison of kinship estimates in Santa Inês sheep using microsatellite and genome-wide SNP markers

• Small microsatellite panels can be useful to genetically improve Santa Inês sheep and to increase meat sheep production. • Microsatellite markers are suitable for kinship estimation in Santa Inês sheep. • Likelihood estimators were the most suitable for kinship estimation using microsatellite markers. • Panels containing a low number of microsatellites showed accuracy similar to a genome-wide SNP panel for kinship analysis. • Santa Inês sheep flocks raised in the Mid-North sub-region of Brazil have a great number of related individuals. The Santa Inês breed stands out in meat sheep production in Brazil. However, this breed is under risk to lose important traits, especially due to pedigree errors and uncontrolled mating. The use of suitable molecular markers can help in the efficient parentage assignment and kinship analysis. In the present study, we aimed to evaluate the power of different numbers of microsatellite markers in comparison to a genome-wide SNP array in kinship estimation in Santa Inês sheep flocks. Blood samples from 257 animals raised in six flocks located in the Mid-North sub-region of Brazil were used for DNA extraction. The microsatellite data were obtained using four panels with different numbers of loci (10, 12, 15, and 19). The panel OvineSNP50 BeadChip (Illumina Inc.) was used for genotyping the animals with SNP data, which were used to calculate the genomic relationship matrix ( G ). The COANCESTRY program was used to propose the best kinship estimator among seven that were tested. The R package RELATED was used to obtain kinship estimates. The kinships obtained using SNPs and microsatellites were compared using descriptive analysis and Pearson correlation. It was possible to estimate relatedness between full siblings, half siblings, parent-offspring, and unrelated animals using the four microsatellite panels. However, panels containing less than 15 markers had lower efficiency. Most of the pairs of individuals were unrelated or half sibs. In the six flocks, several pairs of individuals showed some degree of relatedness. This indicates that a great number of related individuals have mated. Our results demonstrated that kinships estimated using microsatellite panels were highly correlated to those obtained using the SNP panel, with correlations above 0.89. Thus, a low number of microsatellite markers estimates kinship in Santa Inês sheep with similar efficiency to a genome-wide SNP panel.