Editor: Information Resources Management Association Chapter, A New Approach for Sequence Analysi... more Editor: Information Resources Management Association Chapter, A New Approach for Sequence Analysis: Illustrating an Expanded Bioinformatics View through Exploring Properties of the Prestin Protein, co-authored by Kathryn Dempsey Cooper and Hesham Ali, UNO faculty member. As a result of experimental techniques, the combination of biology and computer science was initiated to classify and process an expanding number of biological observations. Bioinformatics: Concepts, Methodologies, Tools, and Applications highlights the area of bioinformatics and its impact over the medical community with its innovations that change how we recognize and care for illnesses. This publication provides significant research and the most recent observations that are useful for researchers, practitioners, and academicians involved in the many aspects of bioinformatics.https://digitalcommons.unomaha.edu/facultybooks/1327/thumbnail.jp
ABSTRACTBalanced chromosomal rearrangements (BCRs), including inversions, translocations, and ins... more ABSTRACTBalanced chromosomal rearrangements (BCRs), including inversions, translocations, and insertions, reorganize large sections of the genome and contribute substantial risk for developmental disorders (DDs). However, the rarity and lack of systematic screening for BCRs in the population has precluded unbiased analyses of the genomic features and mechanisms associated with risk for DDs versus normal developmental outcomes. Here, we sequenced and analyzed 1,420 BCR breakpoints across 710 individuals, including 406 DD cases and the first large-scale collection of 304 control BCR carriers. We found that BCRs were not more likely to disrupt genes in DD cases than controls, but were seven-fold more likely to disrupt genes associated with dominant DDs (21.3% of cases vs. 3.4% of controls; P = 1.60×10−12). Moreover, BCRs that did not disrupt a known DD gene were significantly enriched for breakpoints that altered topologically associated domains (TADs) containing dominant DD genes in c...
SUMMARYRecurrent deletion and duplication of ∼743 kilobases of unique genomic sequence and segmen... more SUMMARYRecurrent deletion and duplication of ∼743 kilobases of unique genomic sequence and segmental duplications at chromosome 16p11.2 underlie a reciprocal genomic disorder (RGD; OMIM 611913 and 614671) associated with neurodevelopmental and psychiatric phenotypes, including intellectual disability, autism spectrum disorder (ASD), and schizophrenia (SCZ). To define molecular alterations associated with the 16p11.2 RGD, we performed transcriptome analyses of mice with reciprocal copy number variants (CNVs) of the syntenic chromosome 7qF3 region and human neuronal models derived from isogenic human induced pluripotent stem cells (hiPSCs) carrying CRISPR-engineered CNVs at 16p11.2. Analysis of differentially expressed genes (DEGs) in mouse cortex, striatum, cerebellum and three non-brain tissues, as well as in human neural stem cells and induced glutamatergic neurons revealed that the strongest and most consistent effects occurred within the CNV sequence, with notable instances of di...
Information Resources Management Association (IRMA) is a research-based professional organization... more Information Resources Management Association (IRMA) is a research-based professional organization dedicated to advancing the concepts and practices of information resources management in modern organizations. IRMA’s primary purpose is to promote the understanding, development and practice of managing information resources as key enterprise assets among IRM/IT professionals. IRMA brings together researchers, practitioners, academicians, and policy makers in information technology management from over 50 countries. Information Resources Management Association (USA)
TP53 mutations are common in colorectal cancer (CRC). Most TP53 sequencing studies have been rest... more TP53 mutations are common in colorectal cancer (CRC). Most TP53 sequencing studies have been restricted to coding regions, but recent studies have revealed that splice mutations can generate transcript variants with distinct tumorigenic and prognostic properties. Here, we performed unrestricted sequencing of all coding sequences and splice regions of TP53 in a single-hospital series of 401 primary CRCs. TP53 splice mutations were detected in 4% of the cases (N = 16), considerably more frequent than reported in major databases, and they were mutually exclusive to exon mutations. RNA sequencing revealed high-level expression of aberrant transcript variants in the majority of splice mutated tumors (75%). Most variants were predicted to produce truncated TP53 proteins, including one sample expressing the potentially oncogenic and druggable p53ψ isoform. Despite heterogeneous transcript structures, downstream transcriptional profiling revealed that TP53 splice mutations had similar effec...
41 The creation of several prestin knock-out and knock-in mouse lines has demonstrated the 42 imp... more 41 The creation of several prestin knock-out and knock-in mouse lines has demonstrated the 42 importance of the intrinsic outer hair cell membrane protein prestin to mammalian hearing. 43 However, the structure of prestin remains largely unknown, with even its major features in 44 dispute. Several studies have suggested that prestin forms homo-oligomers that may be stabilized 45 by disulfide bonds. Our phylogenetic analysis of prestin sequences across chordate classes 46 suggested that the cysteinyl residues could be divided into three groups, depending on the extent 47 of their conservation between prestin orthologs and paralogs or homologs. An alanine scan 48 functional analysis was performed of all nine cysteinyl positions in mammalian prestin. Prestin 49 function was assayed by measurement of prestin-associated non-linear capacitance. Of the nine 50 cysteine-alanine substitution mutations, all were properly membrane-targeted and all 51 demonstrated non-linear capacitance. Four m...
Novel gene and variant discoveries have reached unprecedented scale with the emergence of exome a... more Novel gene and variant discoveries have reached unprecedented scale with the emergence of exome and genome sequencing studies across a spectrum of human disease initiatives. Highly parallelized functional characterization of these variants is now paramount to deciphering disease mechanisms, and approaches that facilitate editing of induced pluripotent stem cells (iPSCs) to derive otherwise inaccessible tissues of interest (e.g., brain) have become critical in genomics research. Here, we sought to facilitate scalable editing of multiple genes and variants by developing a genome engineering approach that incorporates libraries of CRISPR/Cas9 guide RNAs (gRNAs) into a piggyBac (PB) transposon system. To test the efficiency of inducing small indels, targeted deletions, and large reciprocal copy number variants (CNVs), we simultaneously delivered to human iPSCs both Cas9 and a library including 59 single gRNAs targeting segmental duplications, 70 paired gRNAs flanking particular genic re...
ABSTRACTCurrent prenatal and pediatric genetic evaluation requires three tests to capture balance... more ABSTRACTCurrent prenatal and pediatric genetic evaluation requires three tests to capture balanced chromosomal abnormalities (karyotype), copy number variants (microarray), and coding variants (whole exome sequencing [WES] or targeted gene panels). Here, we explored the sensitivity, specificity, and added value of whole genome sequencing (WGS) to displace all three conventional approaches. We analyzed single nucleotide variants, small insertions and deletions, and structural variants from WGS in 1,612 autism spectrum disorder (ASD) quartet families (n=6,448 individuals) to benchmark the diagnostic performance of WGS against microarray and WES. We then applied these WGS variant discovery and interpretation pipelines to 175 trios (n=525 individuals) with a fetal structural anomaly (FSA) detected on ultrasound and pre-screened by karyotype and microarray. Analyses of WGS in ASD quartets identified a diagnostic variant in 7.5% of ASD probands compared to 1.1% of unaffected siblings (odd...
Methods in molecular biology (Clifton, N.J.), 2019
Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prena... more Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prenatal genome abnormalities. The two most ubiquitous traditional methods for prenatal SV assessment, karyotyping and chromosomal microarrays, do not provide sufficient resolution for some clinically actionable SVs. Standard whole-genome sequencing (WGS) overcomes shortcomings of traditional techniques by providing base-pair resolution of the entire accessible genome. However, while sequencing costs have continued to decline in recent years, conventional WGS costs remain high for most routine clinical applications. Here, we describe a specialized WGS technique using large inserts (liWGS; also known as "jumping libraries") to resolve large (>5000-10,000 nucleotides) SVs at kilobase-resolution in prenatal samples, and at a fraction of the cost of standard WGS. We explicate the protocols for generating liWGS libraries and supplement with an overview for processing and analyzing liW...
Whole-genome sequencing (WGS) has facilitated the first genome-wide evaluations of the contributi... more Whole-genome sequencing (WGS) has facilitated the first genome-wide evaluations of the contribution of de novo noncoding mutations to complex disorders. Using WGS, we identified 255,106 de novo mutations among sample genomes from members of 1902 quartet families in which one child, but not a sibling or their parents, was affected by autism spectrum disorder (ASD). In contrast to coding mutations, no noncoding functional annotation category, analyzed in isolation, was significantly associated with ASD. Casting noncoding variation in the context of a de novo risk score across multiple annotation categories, however, did demonstrate association with mutations localized to promoter regions. We found that the strongest driver of this promoter signal emanates from evolutionarily conserved transcription factor binding sites distal to the transcription start site. These data suggest that de novo mutations in promoter regions, characterized by evolutionary and functional signatures, contribu...
Editor: Information Resources Management Association Chapter, A New Approach for Sequence Analysi... more Editor: Information Resources Management Association Chapter, A New Approach for Sequence Analysis: Illustrating an Expanded Bioinformatics View through Exploring Properties of the Prestin Protein, co-authored by Kathryn Dempsey Cooper and Hesham Ali, UNO faculty member. As a result of experimental techniques, the combination of biology and computer science was initiated to classify and process an expanding number of biological observations. Bioinformatics: Concepts, Methodologies, Tools, and Applications highlights the area of bioinformatics and its impact over the medical community with its innovations that change how we recognize and care for illnesses. This publication provides significant research and the most recent observations that are useful for researchers, practitioners, and academicians involved in the many aspects of bioinformatics.https://digitalcommons.unomaha.edu/facultybooks/1327/thumbnail.jp
ABSTRACTBalanced chromosomal rearrangements (BCRs), including inversions, translocations, and ins... more ABSTRACTBalanced chromosomal rearrangements (BCRs), including inversions, translocations, and insertions, reorganize large sections of the genome and contribute substantial risk for developmental disorders (DDs). However, the rarity and lack of systematic screening for BCRs in the population has precluded unbiased analyses of the genomic features and mechanisms associated with risk for DDs versus normal developmental outcomes. Here, we sequenced and analyzed 1,420 BCR breakpoints across 710 individuals, including 406 DD cases and the first large-scale collection of 304 control BCR carriers. We found that BCRs were not more likely to disrupt genes in DD cases than controls, but were seven-fold more likely to disrupt genes associated with dominant DDs (21.3% of cases vs. 3.4% of controls; P = 1.60×10−12). Moreover, BCRs that did not disrupt a known DD gene were significantly enriched for breakpoints that altered topologically associated domains (TADs) containing dominant DD genes in c...
SUMMARYRecurrent deletion and duplication of ∼743 kilobases of unique genomic sequence and segmen... more SUMMARYRecurrent deletion and duplication of ∼743 kilobases of unique genomic sequence and segmental duplications at chromosome 16p11.2 underlie a reciprocal genomic disorder (RGD; OMIM 611913 and 614671) associated with neurodevelopmental and psychiatric phenotypes, including intellectual disability, autism spectrum disorder (ASD), and schizophrenia (SCZ). To define molecular alterations associated with the 16p11.2 RGD, we performed transcriptome analyses of mice with reciprocal copy number variants (CNVs) of the syntenic chromosome 7qF3 region and human neuronal models derived from isogenic human induced pluripotent stem cells (hiPSCs) carrying CRISPR-engineered CNVs at 16p11.2. Analysis of differentially expressed genes (DEGs) in mouse cortex, striatum, cerebellum and three non-brain tissues, as well as in human neural stem cells and induced glutamatergic neurons revealed that the strongest and most consistent effects occurred within the CNV sequence, with notable instances of di...
Information Resources Management Association (IRMA) is a research-based professional organization... more Information Resources Management Association (IRMA) is a research-based professional organization dedicated to advancing the concepts and practices of information resources management in modern organizations. IRMA’s primary purpose is to promote the understanding, development and practice of managing information resources as key enterprise assets among IRM/IT professionals. IRMA brings together researchers, practitioners, academicians, and policy makers in information technology management from over 50 countries. Information Resources Management Association (USA)
TP53 mutations are common in colorectal cancer (CRC). Most TP53 sequencing studies have been rest... more TP53 mutations are common in colorectal cancer (CRC). Most TP53 sequencing studies have been restricted to coding regions, but recent studies have revealed that splice mutations can generate transcript variants with distinct tumorigenic and prognostic properties. Here, we performed unrestricted sequencing of all coding sequences and splice regions of TP53 in a single-hospital series of 401 primary CRCs. TP53 splice mutations were detected in 4% of the cases (N = 16), considerably more frequent than reported in major databases, and they were mutually exclusive to exon mutations. RNA sequencing revealed high-level expression of aberrant transcript variants in the majority of splice mutated tumors (75%). Most variants were predicted to produce truncated TP53 proteins, including one sample expressing the potentially oncogenic and druggable p53ψ isoform. Despite heterogeneous transcript structures, downstream transcriptional profiling revealed that TP53 splice mutations had similar effec...
41 The creation of several prestin knock-out and knock-in mouse lines has demonstrated the 42 imp... more 41 The creation of several prestin knock-out and knock-in mouse lines has demonstrated the 42 importance of the intrinsic outer hair cell membrane protein prestin to mammalian hearing. 43 However, the structure of prestin remains largely unknown, with even its major features in 44 dispute. Several studies have suggested that prestin forms homo-oligomers that may be stabilized 45 by disulfide bonds. Our phylogenetic analysis of prestin sequences across chordate classes 46 suggested that the cysteinyl residues could be divided into three groups, depending on the extent 47 of their conservation between prestin orthologs and paralogs or homologs. An alanine scan 48 functional analysis was performed of all nine cysteinyl positions in mammalian prestin. Prestin 49 function was assayed by measurement of prestin-associated non-linear capacitance. Of the nine 50 cysteine-alanine substitution mutations, all were properly membrane-targeted and all 51 demonstrated non-linear capacitance. Four m...
Novel gene and variant discoveries have reached unprecedented scale with the emergence of exome a... more Novel gene and variant discoveries have reached unprecedented scale with the emergence of exome and genome sequencing studies across a spectrum of human disease initiatives. Highly parallelized functional characterization of these variants is now paramount to deciphering disease mechanisms, and approaches that facilitate editing of induced pluripotent stem cells (iPSCs) to derive otherwise inaccessible tissues of interest (e.g., brain) have become critical in genomics research. Here, we sought to facilitate scalable editing of multiple genes and variants by developing a genome engineering approach that incorporates libraries of CRISPR/Cas9 guide RNAs (gRNAs) into a piggyBac (PB) transposon system. To test the efficiency of inducing small indels, targeted deletions, and large reciprocal copy number variants (CNVs), we simultaneously delivered to human iPSCs both Cas9 and a library including 59 single gRNAs targeting segmental duplications, 70 paired gRNAs flanking particular genic re...
ABSTRACTCurrent prenatal and pediatric genetic evaluation requires three tests to capture balance... more ABSTRACTCurrent prenatal and pediatric genetic evaluation requires three tests to capture balanced chromosomal abnormalities (karyotype), copy number variants (microarray), and coding variants (whole exome sequencing [WES] or targeted gene panels). Here, we explored the sensitivity, specificity, and added value of whole genome sequencing (WGS) to displace all three conventional approaches. We analyzed single nucleotide variants, small insertions and deletions, and structural variants from WGS in 1,612 autism spectrum disorder (ASD) quartet families (n=6,448 individuals) to benchmark the diagnostic performance of WGS against microarray and WES. We then applied these WGS variant discovery and interpretation pipelines to 175 trios (n=525 individuals) with a fetal structural anomaly (FSA) detected on ultrasound and pre-screened by karyotype and microarray. Analyses of WGS in ASD quartets identified a diagnostic variant in 7.5% of ASD probands compared to 1.1% of unaffected siblings (odd...
Methods in molecular biology (Clifton, N.J.), 2019
Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prena... more Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prenatal genome abnormalities. The two most ubiquitous traditional methods for prenatal SV assessment, karyotyping and chromosomal microarrays, do not provide sufficient resolution for some clinically actionable SVs. Standard whole-genome sequencing (WGS) overcomes shortcomings of traditional techniques by providing base-pair resolution of the entire accessible genome. However, while sequencing costs have continued to decline in recent years, conventional WGS costs remain high for most routine clinical applications. Here, we describe a specialized WGS technique using large inserts (liWGS; also known as "jumping libraries") to resolve large (>5000-10,000 nucleotides) SVs at kilobase-resolution in prenatal samples, and at a fraction of the cost of standard WGS. We explicate the protocols for generating liWGS libraries and supplement with an overview for processing and analyzing liW...
Whole-genome sequencing (WGS) has facilitated the first genome-wide evaluations of the contributi... more Whole-genome sequencing (WGS) has facilitated the first genome-wide evaluations of the contribution of de novo noncoding mutations to complex disorders. Using WGS, we identified 255,106 de novo mutations among sample genomes from members of 1902 quartet families in which one child, but not a sibling or their parents, was affected by autism spectrum disorder (ASD). In contrast to coding mutations, no noncoding functional annotation category, analyzed in isolation, was significantly associated with ASD. Casting noncoding variation in the context of a de novo risk score across multiple annotation categories, however, did demonstrate association with mutations localized to promoter regions. We found that the strongest driver of this promoter signal emanates from evolutionarily conserved transcription factor binding sites distal to the transcription start site. These data suggest that de novo mutations in promoter regions, characterized by evolutionary and functional signatures, contribu...
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