53, 15271533 (2021). ASD-eQTLs within the fetal cortex PPI aminoacyl-tRNA biosynthesis cluster are associated with: (a) increases in transcript levels for five genes (i.e. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene's function. *_merged_nodups.txt files) were processed to obtain Hi-C chromatin interaction libraries in the following format: read name, str1, chr1, pos1, frag1 mapq1, str2, chr2, pos2, frag2, mapq2 (str=strand, chr=chromosome, pos=position, frag=restriction site fragment, mapq=mapping quality score, 1 and 2 correspond to read ends in a pair). Raw Hi-C data were downloaded from dbGaP (accession: phs001190.v1.p1) and GEO (https://www.ncbi.nlm.nih.gov/geo/, accession: GSE87112) and analyzed using Juicer (v1.5)75 (https://github.com/aidenlab/juicer) pipeline to generate Hi-C libraries. Similar changes occur in adult cortex where transcript levels for 15 genes are upregulated in association with a change to the minor allele at the eQTL SNP (Fig. Genes that have been curated as being involved in ASD (AutDB31; http://autism.mindspec.org/autdb/Welcome.do, assessed on 16/11/2020). Front. Science 366, 11341139 (2019). RNA-seq data)20,21 were mapped to gene identifiers, thus there was a potential loss of data specificity, since genes typically produce multiple transcripts and protein variants due to alternative splicing. These spatial interactions are dynamic, developmentally and temporally dependent13. We define a well-powered list of 2,320 sex-het SNPs showing sex-heterogeneity across multiple traits. 51, 11601169 (2019). We identified 80 eQTLs that are involved in 131 significant spatial eQTL-eGene interactions in fetal cortex; and 58 eQTLs that are associated with 67 significant spatial eQTL-eGene interactions in adult cortex (Fig. Therefore, the aims of the present study were to determine the TCOF1 gene's core promoter and to identify mutations in this region that could contribute to the phenotypic variation observed in this syndrome. Writing Committee for the Attention-Deficit/Hyperactivity Disorder et al. ADS Identifying Liver Cancer-Related Enhancer SNPs by Integrating - PubMed 1, Supplementary Table 3). 47, D607D613 (2019). Robinson, E. B. et al. The site is secure. National Library of Medicine From these CSPPI networks we identified 42 ASD-associated PPIs within the fetal gene set, and 10 ASD-associated PPIs from the adult cortical tissue gene set (Fig. Genome Res. This site needs JavaScript to work properly. PubMed The mutational constraint spectrum quantified from variation in 141,456 humans. Use the Previous and Next buttons to navigate the slides or the slide controller buttons at the end to navigate through each slide. 2009;29(5):286-91. doi: 10.1080/10799890902911948. PDF GENETIC ASSOCIATION STUDIES OF COMPLEX DISEASES ByYen - arXiv Quality control metrics and gene-level expression data were calculated using RNA-seQC (v2.3.6) on the basis of GENCODE v26 gene annotation (gencode.v26.GRCh38.genes.gtf, gs://gtex-resources). Author summary Risk for many diseases and related manifestations differs by sex. https://doi.org/10.1038/s41588-022-01087-y (2022). Genes that have been curated as being involved in ASD (AutDB31; http://autism.mindspec.org/autdb/Welcome.do, assessed on 16/11/2020). Am. Single-Nucleotide Polymorphism - an overview | ScienceDirect Topics eQTL datasets for fetal and adult cortex were obtained from Walker et al.20 and GTEx v821, correspondingly. The authors declare no competing interests. The proportion of ASD explained by SNPs has been estimated to be between 17 and 60%7,8, thus their contribution should not be neglected. Autism 3, 9 (2012). Ensembl protein (STRING)33 and transcript identifiers (GTEx and Walker et al. A common two-phase adipogenesis process is described: early determination and terminal differentiation phases, involving an intricate integration of cytoarchitecture, transcription factors and co-regulators, and signaling pathways. CAS Genomic and metabolic profiling of two tomato contrasting cultivars for tolerance to Tuta absoluta. A. Sey, Benxia Hu, Hyejung Won, Anja Barei, Alexander Jolyon Nash, Boris Lenhard, Gokul Ramaswami, Hyejung Won, Daniel H. Geschwind, Michael J. Gandal, Jillian R. Haney, Daniel H. Geschwind, Mirolyuba Ilieva, Blanca Irene Aldana, Tanja Maria Michel, Jhih-Rong Lin, Yingjie Zhao, Zhengdong D. Zhang, Esra Sefik, Ryan H. Purcell, Jennifer G. Mulle, Scientific Reports 1). Fifteen of these shared eQTLs control the same eGenes in fetal and adult cortex (e.g. Van Rooij, D. et al. We obtained ASD-associated SNPs from nine GWAS studies that were performed in cohorts containing individuals of mostly European ancestry (Supplementary Table 2). & Deptua, W. Butyrophilins: An important new element of resistance. Cells 8, 788 (2019). The https:// ensures that you are connecting to the miRNA) or by spatial associations of the regulatory element and target gene. Virtual histology of cortical thickness and shared neurobiology in 6 psychiatric disorders. Neuropsychol. This approach, in combination with clinical studies on ASD, will contribute to individualized mechanistic understanding of ASD development. Lettre, G. One step closer to linking GWAS SNPs with the right genes. EG is the recipient of a Liggins Ph.D. scholarship and was supported by MBIE Catalyst Grant (The New ZealandAustralia LifeCourse Collaboration on Genes, Environment, Nutrition and Obesity (GENO); UOAX1611). 3). Huang C, Guo Y, Li W, Xiang B, Zeng J, Zhou F, She L, Zhang P, Wang S, Liu B, Dai Q, Yang M. BMJ Open Diabetes Res Care. By contrast, the ASD-eQTL associations within the fetal cortex PPI fatty acid metabolism and spliceosome clusters are less complex (decreases: FADS1, TBL1X, SF3B1, or increases: FADS2, DHX38 and THOC7; Fig. Adult and fetal cortex-specific PPIs (CSPPI) were generated. Since the output is an easily manipulated spreadsheet, the user can sort the SNPs to highlight different SNP features. eCollection 2022. Each SNP represents a difference in a single DNA building block, called a "nucleotide." For example, an SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA. This method prioritizes genes for functional characterization and helps address questions about the architecture of human phenotypes. Nat. Mech. How could SNPs contribute to gene regulation quizlet? Single Nucleotide Polymorphisms (SNPs) - Genome.gov Hi-C libraries) and cortex-specific eQTLs to identify how ASD-associated SNPs impact cortex-specific gene expression. 3). Fetal and adult ASD-associated eQTLs were also associated with schizophrenia, unipolar depression, ADHD, bipolar disorder, anorexia nervosa and obsessivecompulsive disorder (Supplementary Fig. Chapter Only Hi-C libraries that contain >90% alignable unique read pairs, and >50% unique contacts (<40% duplication rate) within the total sequenced read pairs were included in the analysis. Solution 5 (1 Ratings ) Solved Biology 3 Years Ago 40 Views This Question has Been Answered! ASD-associated SNPs (p<5108, n=454) were downloaded from the GWAS Catalog (Supplementary Tables 1 and 2). We have shown that the transcript levels of genes, whose encoded proteins are known to contribute to immune pathways, fatty acid metabolism, ribosome biogenesis, aminoacyl-tRNA biosynthesis and spliceosome are affected in the fetal cortex. PubMed Nutritional Intervention Preconception and During Pregnancy to Maintain Healthy Glucose Metabolism and Offspring Health (NiPPeR): Study protocol for a randomised controlled trial. 3). Sci Rep 11, 15867 (2021). Therefore, characterizing the functional impacts (i.e. 45, D896D901 (2017). The remaining 60% of the identified eQTLs involve interactions with non-adjacent genes that can be >1Mb away in the linear DNA sequence or even on a different chromosome. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Article 3, 1 (2011). Schmitt, A. D. et al. In order to study spatial regulatory interactions in fetal and adult cortical tissues, we analysed two fetal brain-specific (i.e. & Kellis, M. Chromatin-state discovery and genome annotation with ChromHMM. 19, 13211330 (2016). A functional SNP in the promoter region of TCOF1 is associated - PubMed enhancer reporter assays); (b) confirm that the Polycomb complexes are responsible for the observed activity (e.g. Science 376, eabf3041 (2022). [Structural variation in the human genome contributes to variation of traits]. Hum. (c) All ASD-associated eQTLs in adult cortex (n=58) and approximately 78 (97.5%) of the ASD-associated eQTLs within the fetal cortex are located within non-coding genomic regions (Supplementary Table 5). Firstly, SNPs can mark regulatory regions that affect distant genes (i.e. J. Immunol. In the meantime, to ensure continued support, we are displaying the site without styles Basically, SNPs are copying errors. Article Breastfeed. Brandler, W. M. et al. Neurosignals 18, 98112 (2010). (e) Most of the fetal ASD-associated eQTLs are located within quiescent/low transcribed, week repressed PolyComb, repressed PolyComb and weak transcription regions. Google Scholar. This work was funded by a University of Auckland FRDF Grant (Confirming spatial connections to unravel how SNPs affect phenotype; 3714499) and a MBIE Catalyst grant (The New Zealand-Australia LifeCourse Collaboration on Genes, Environment, Nutrition and Obesity (GENO); UOAX1611) to JOS. Formulate hypotheses Expert Answer 100% (1 rating) Answer : 1 : In an indivisual the protein expression is regulated by higher and lower methods . D'Esposito D, Guadagno A, Amoroso CG, Cascone P, Cencetti G, Michelozzi M, Guerrieri E, Ercolano MR. Planta. As expected, the majority of identified eQTLs were located within intronic and intergenic regions (Fig. Nat. Nott, A. et al. ZSCAN23 and LY6G5C) whose transcript levels increase or decrease, dependent upon specific eQTL. Next, the CoDeS3D algorithm identified the restriction fragments interacting with the SNP-containing restriction fragments. 49, 433436 (2012). Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations. 344 ASD-associated SNPs (p<5108) represented in both fetal and adult cortex-specific eQTL datasets were run through the CoDeS3D pipeline to identify 81 and 44 spatially regulated genes in fetal and adult cortical tissues, correspondingly. At the same time, ASD-eQTLs are also associated with regulation of fatty acid metabolism, ribosome biogenesis, aminoacyl-tRNA biosynthesis and spliceosome pathways in fetal cortex. Dysregulation of fatty acid metabolism in early brain development may be a risk factor or marker for early-onset of ASD48. Single nucleotide polymorphisms (SNPs) are one of the most common types of genetic variations in the human genome. Roles for these component gene expression processes in ASD are supported by existing studies (e.g. J. Med. Schematic representation of the procedure to map SNPs to regulatory elements and target genes. 4). 20, 327348 (2010). As such, the three-dimensional (3D) genome organization, which emerges from the sum of the biophysical interactions within the nucleus, includes tissue-specific spatial interactions between eQTL regions and the genes that they control (hereafter eGenes)12. A reference panel of 64,976 haplotypes for genotype imputation. and JavaScript. Sample-level gene read and TPM (Transcripts Per kilobase Million) counts were concatenated using combine_GCTs.py. Nucleic Acids Res. 45, 984994 (2013). Google Scholar. Transl. Science 360, 327331 (2018). Cell. Phenotypes were defined as the mapped traits associated with the SNP in the GWAS Catalog. For example, PRC1.5 is recruited to activate genes47 and in combination with AUTS2 (autism susceptibility candidate 2) activates gene expression in neurons47. Variants that do not have strand information for HumanOmni25-8v1-2_A1 and HumanOmni2-5Exome-8-v1-1-A genotyping chips were excluded (strand files and update_build.sh script were downloaded from https://www.well.ox.ac.uk/~wrayner/strand/, 01/07/2020, Supplementary Table 1). We identified 42 PPIs in the fetal and 10 PPIs in the adult cortical tissues. To obtain 9, 5198 (2018). Nat. Rau, S. et al. Lancet 383, 896910 (2014). Willsey, A. J. et al. Gene expression is the outcome of numerous processes including transcription, co-transcriptional splicing, mRNA export, and translation. Frontiers | From GWAS to Function: Using Functional Genomics to By contrast, 9 fetal cortex-specific genes (i.e. J.O.S. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Gene expression variation can be seen across all levels of organismal organization (i.e. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in There was significant enrichment (p<0.01, permutation test: 1000) of ASD-associated eQTLs within loci repressed by Polycomb proteins in the fetal cortex when compared to the adult cortex. The p value was calculated as the sum of these instances divided by the total number of iterations n. If the p<0.01 we assume that the observed relationship is non-random. Reads where both ends had a mapq30 were included in the final library. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. All genomic positions and SNP annotations were obtained for human genome reference build hg38 (GRCh38) release 75. RNA-seq data were processed by GTEx using RNA-seq analysis (https://github.com/broadinstitute/gtex-pipeline/tree/master/rnaseq) and eQTL discovery (https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) pipelines to calculate normalized gene expression and covariates. Collectively, our results provide insight into potential cortex-specific regulatory mechanisms and pathways through which ASD-associated SNPs can contribute to the development and maintenance of ASD. Science 342, 253257 (2013). Thus, integrating biological measurements on developmental and tissue-specific spatial chromatin interactions with eQTL information could inform our understanding of the regulatory impacts of ASD-associated SNPs. Nature 599, 628634 (2021). You are using a browser version with limited support for CSS. 3, Supplementary Table 4). Nature 581, 434443 (2020). Single nucleotide polymorphism (SNP) is the simplest form of DNA variation among individuals. PGBD1, ZKSCAN7, MPHOSPH9, TCF19 and VWA7); (b) decreases in transcript levels for VARS2; and (c) two genes (i.e. Thereby, SNPs contribute to disease susceptibility, various responses to medication treatment and differences in outcomes within a disease population [8, 9]. To build ASD-specific fetal and adult CSPPIs, only interactions between ASD-associated genes we extracted from fetal and adult CSPPIs. Enrichment analyses were performed using R package regioneR79 (permutation test: 1000). Szklarczyk, D. et al. Transl. PubMedGoogle Scholar. (b) Thirty ASD-associated SNPs are eQTLs in both fetal and adult cortical tissues. As such, restriction fragments were used to identify regulatory interactions between SNPs and genes (Fig. They can act as biological markers, helping scientists locate genes that are associated with disease. CAS However, this would require randomised control trials in animals prior to testing in humans. MeSH 2009 May;37(5):977-91. doi: 10.1124/dmd.108.026047. Westra, H.-J. 25, 142154 (2015). 2d). ASD-associated eQTLs regulate 81 genes in fetal and 44 genes in adult cortical tissues (Fig. Question: how could SNP's contribute to gene regulation? - Chegg Golovina, E., Fadason, T., Lints, T.J. et al. 11, 27 (2017). Notably, these regulatory elements are only associated with the expression (eQTL or expression quantitative trait locus) of the adjacent gene in ~40% of cases11. 2002;47(11):561-6. doi: 10.1007/s100380200086. J. Psychiatry 175, 359369 (2018). & Zhang, Z. Bauer, D. E. et al. SNPs represent an important class of genetic variant, defined as a single-base change in the DNA sequence. The pipeline included BWA (v0.7.15) alignment of paired-end reads onto the hg38 reference genome, merging paired-end read alignments and removing chimeric, unmapped and duplicated reads. Usui, N. et al. volume11, Articlenumber:15867 (2021) SNPs can also be used to track the inheritance of disease genes within families. 69, 101468 (2020). Roles for immune dysfunction in ASD etiology are increasingly being identified57,58,59. PRC2-associated chromatin contacts in the developing limb reveal a possible mechanism for the atypical role of PRC2 in HoxA gene expression. Nat. Only SNPs associated with ASD with a p<5108 were included in downstream analyses. Wang J, Su W, Zhang T, Zhang S, Lei H, Ma F, Shi M, Shi W, Xie X, Di C. Cell Death Dis. APOPT1, AS3MT) with the ASD-eQTL. 235, 40314045 (2020). We identified changes within multiple key component pathways of gene expression (i.e. & Crawford, D. A. Rare genetic susceptibility variants assessment in autism spectrum disorder: Detection rate and practical use. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Consistent with this, we identified that ASD-associated genetic variants impact transcript levels for genes involved in fatty acid metabolism in the developing fetal cortex (1421 postconceptional weeks). FOIA Nat. And by View the full answer These SNPs mostly locate within a gene or in a regulatory region near a gene and can affect the gene's function to Asthma-associated SNPs and genes from GWAS catalog. 2e). Diagnostic and Statistical Manual of Mental Disorders (DSM-5 (R)) (American Psychiatric Association Publishing, 2013). The Kyoto Encyclopedia of Genes and Genomes (KEGG) database34 was used to query the most impacted biological pathways. & Anderson, M. P. T lymphocytes and cytotoxic astrocyte blebs correlate across autism brains. Cis-eQTL SNPs are the SNPs that are within or around the corresponding gene, and trans-eQTL SNPs are those that are far away or even on dierent chromosomes. You'll get a detailed solution from a subject matter expert that helps you learn core concepts. CrossMap (v0.2.6) was used to convert coordinates of genetic variants from genome build hg19 to hg38, resulting in ~54.8 million genetic variants. Aguet, F. et al. eGene enrichment was tested within the biological process, molecular function and cellular component GO terms. Therefore, with appropriate pre-natal genetic diagnosis of risk and patient stratification, it remains possible that targeted lipid supplementation could reduce the risk of ASD. rSNPBase 3.0: an updated database of SNP-related regulatory elements Genet. 1). Five genes within this cluster (i.e. Protoc. Transcript levels for four genes: (a) increased (i.e. 3). These findings indicate that there may be developmental stage-specific differences in the impact of the immune system on ASD risk and on-going severity. Genes whose transcript levels are associated with a trans-acting ASD-associated eQTL. Google Scholar. Porokhovnik, L. Individual copy number of ribosomal genes as a factor of mental retardation and autism risk and severity. Keller, R.) 89110 (Springer International Publishing, 2019). Med. Cell 167, 1481-1494.e18 (2016). Article Grove, J. et al. g:Profiler: A web server for functional enrichment analysis and conversions of gene lists (2019 update). 3). 3). A novel candidate gene CLN8 regulates fat deposition in avian CAS By submitting a comment you agree to abide by our Terms and Community Guidelines. Top five genotype principal components (calculated using compute_genotype_pcs.py script from https://github.com/broadinstitute/gtex-pipeline/tree/master/genotype), 30 PEER factors, sex and genotyping platform were used as covariates in the eQTL analysis. KLC1, ZSCAN31 and TRIM26), or decreased (i.e. Boyle, E. A., Li, Y. I. 3). Nat. However, more than 84% of the identified spatially regulated genes were novel and have not previously been linked to autism or curated in AutDB. 51, 431444 (2019). The regulatory effects can occur in trans (e.g. Article Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. A single nucleotide polymorphism, or SNP (pronounced "snip"), is a variation at a single position in a DNA sequence among individuals. Cell 155, 9971007 (2013). Notably, the transcript levels for 6 genes in the fetal immune cluster (HCG27, TAP2, HLA-F, HLA-DMA, HLA-C and HLA-DMB) are associated with regulation by Polycomb-repressed ASD-eQTLs. The SNPs located in enhancer elements may affect gene expression and lead to disease. Tamiji, J. [34] Genome-wide genetic data can be generated by multiple technologies, including SNP array and whole genome sequencing. Hi-C data) enables the identification of novel local and distal eQTL-gene connections. PubMed There are several reasons for this: (1) there are multiple potential mechanisms through which a genetic variant can impact on a phenotype. Changes to genes within the immune-related processes within adult cortex mostly affect the processing of exogenous antigen. Autism Spectr. Synaptic Neurosci. However, the remaining 15 eQTLs are associated with different eGenes in adult and fetal cortical tissues (Supplementary Table 4). chr1_61170_C_T_b38 where chr1 is chromosome name, 61170 is variant position on the chromosome, C is reference allele, T is alternate allele and b38 is genome build 38). TYW5, FTCDNL1, and RTN1) whose transcript levels decrease with the ASD-eQTL and NDRG4, whose transcript levels increase or decrease dependent upon the ASD-eQTL. Google Scholar. Genes and environments, development and time | PNAS Neurol. van Arensbergen, J. et al. aberrant splicing and ASD52,53; upregulation of ribosomal protein genes and a higher ribosomal gene dosage can be linked to ASD risk and severity54,55). These simple changes can be of transition or transversion type and they occur throughout the genome at a frequency of about one in 1,000 bp. identified a form of ASD resulting from a failure of the brain to properly import amino acidsa critical substrate in gene expression56. Over the past decade, genome-wide association (GWAS) and genetic studies have identified increasing numbers of single nucleotide polymorphisms (SNPs)3,4 and other forms of variation (e.g., copy number variants, rare structural variants)5,6 that are associated with ASD. Article the effects of rs7432375 and rs7618871 on PCCB gene transcript levels are not collinear; Supplementary Fig. J. Stat. Kumar, S., Ambrosini, G. & Bucher, P. SNP2TFBSA database of regulatory SNPs affecting predicted transcription factor binding site affinity. Grossniklaus, U. ISSN 2045-2322 (online). HLA-DRB1, HLA-DMB and HLA-DMA; associated with exogenous peptide processing) genes. The resulting CSPPI networks contained 1,784,342 PPIs between 17,156 unique proteins in the adult brain, and 1,690,571 PPIs between 16,519 unique proteins in the fetal brain. 2, Supplementary Table 5). Secondly, in our manuscript we focused on cortex-specific eQTL-gene connections. DiStasio, M. M., Nagakura, I., Nadler, M. J. Genotypes, expression matrices and covariates for fetal and adult brain were integrated into CoDeS3D11 (https://github.com/Genome3d/codes3d-v2) pipeline as two separate eQTL databases. Chang, X. 12, 230 (2018). Nucleic Acids Res. 4, 334336 (2011). For SNPs analysis, we resampled SNPs from the list of all GWAS SNPs with gwas p<5108. What are SNPs and Why Are They Important? - Gene Food J. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Similarly, the ribosome biogenesis in eukaryotes cluster contained ASD-eQTL associated genes whose transcripts were increased (n=5), decreased (n=4), and one that was subject to increases or decreases in transcript levels depending on specific ASD-eQTL. 4, Supplementary Table 9). They may be responsible for the diversity among individuals, geno SNPs: impact on gene function and phenotype This improved knowledge may provide a starting point for the development of new, useful SNP markers for medical testing and a safer individualized medication to treat the most common devastating disorders. and JavaScript. CAS Rev. Enhancer elements are functional segments of DNA located in noncoding regions that play an important role in regulating gene expression. When SNPs are located near a gene, then it is postulated that the gene contributes to the variation under investigation. However, despite having the same effects in fetal and adult tissues, some eQTLs had opposite direction of effects on the gene of interest (e.g. When SNPs occur within a gene or in a regulatory region near a gene, they often play a more direct role in the disease by affecting the function of the gene, either causing it to make a protein that works too well, or has less activity than normal, or completely stops its production. MATH Nat. by chromatin immunoprecipitation); and (c) identify the Polycomb subunits that differentiate those sites that enhance or repress transcription within the developing cortex. Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population. Of 454 ASD-associated SNPs, 344 SNPs were represented in both fetal and adult cortex eQTL databases, and were run through the CoDeS3D pipeline (Fig. Genet. Question : How could SNPs contribute to gene regulation? Formulate eCollection 2022. Mahfouz, A., Ziats, M. N., Rennert, O. M., Lelieveldt, B. P. F. & Reinders, M. J. T. Shared pathways among autism candidate genes determined by co-expression network analysis of the developing human brain transcriptome. For gene analysis, we resampled eGenes from the list of all genes in the genome (GENCODE transcript model version 26). 47, W191W198 (2019). Genom. Notably, Polycomb repressive complexes have distinct regulatory roles in identity, proliferation and differentiation of neuronal progenitor cells during development29,30. Rev. 2e). Psychiatry 11, 71 (2021). Genet. . BCFtools (v1.10.2) was used to exclude genetic variants on chromosome 0 (omitted due to mapping to multiple locations) and chromosome 25 (XY pseudoautosomal region), to rename chromosomes 23 (X), 24 (Y) and 26 (MT), to fix REF allele, to check samples sex and to normalize the output vcf file to the GRCh37 reference genome (human_g1k_v37.fasta.gz, downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/, 01/07/2020). 8 from fetal cortex: DDHD2, HLA-DRB1, PCCB, PCDH15, SF3B1, SNX19, TBL1X, VWA7; and 7 from adult cortex: DDHD2, GALNT10, PBX1, PCCB, RERE, SF3B1, SNX19) had been previously linked to ASD (Fig.
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