Kusuma Lingaiah - Academia.edu (original) (raw)

Papers by Kusuma Lingaiah

Research paper thumbnail of Analysis of genetic variability among bivoltine and multivoltine silkworm genotypes using inter simple sequence repeat and simple sequence repeat markers

Research paper thumbnail of An insight into the understanding of 5-HTR2A variants leading to schizophrenia

PubMed, Dec 1, 2014

Schizophrenia is one of the most important mental disorders which is characterized by a deep disr... more Schizophrenia is one of the most important mental disorders which is characterized by a deep disruption of the thinking process and of emotional response1. It is a disabling group of brain disorders that has symptoms of hallucinations, delusions, disorganized communication, poor planning, reduced motivation and blunted affect2. The incidence of schizophrenia is relatively low (median value 15.2 per 100,000/year) and is one of the major contributors to the global burden of disease2,3. In India, the prevalence of schizophrenia is estimated to be about 3/1000 individuals4,5. Advances in genetics of schizophrenia research have established the significance of genes in aetiology, but have not identified the main relationship between observed genetic risks and specific DNA variants, protein alterations or biological processes6.

Research paper thumbnail of Identifying the risk of producing aneuploids using meiotic recombination genes as biomarkers: A copy number variation approach

Indian Journal of Medical Research, 2017

Background & objectives: Aneuploids are the most common chromosomal abnormality in liveborns and ... more Background & objectives: Aneuploids are the most common chromosomal abnormality in liveborns and are usually the result of non-disjunction (NDJ) in meiosis. Copy number variations (CNVs) are large structural variations affecting the human genome. CNVs influence critical genes involved in causing NDJ by altering their copy number which affects the clinical outcome. In this study influence of CNVs on critical meiotic recombination was examined using new computational technologies to assess their role in causing aneuploidy. Methods: This investigation was based on the analysis of 12 random normal populations consisting of 1714 individuals for aneuploid causing genes under CNV effect. To examine the effect of CNVs on genes causing aneuploidy, meiotic recombination genes were analyzed using EnrichR, WebGestalt and Ingenuity Pathway Analysis (IPA). Results: Forty three NDJ genes were found under CNV burden; IPA (Ingenuity Pathway Analysis) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of CNV in meiotic recombination genes revealed a significant role of breast cancer gene 1, amyloid protein precursor, mitogen-activated protein kinase and nerve growth factor as key molecular players involved in causing aneuploidy. Interaction between these genes with other CNV-overlapping genes involved in cell cycle, recombination and meiosis might lead to increased incidences of aneuploidy. Interpretation & conclusions: The findings of this study implied that the effect of CNVs on normal genome contributed in amplifying the occurrences of chromosomal aneuploidies. The normal individuals consisting of variations in the susceptible genes causing aneuploids in the population remain undetected until the disorder genes express in the succeeding generations.

Research paper thumbnail of CNV map and phylogenetic tree

PLOS ONE, Apr 24, 2015

<p>a) CNV map of 379 shared CNVs across all chromosomes and populations<b>.</b>... more <p>a) CNV map of 379 shared CNVs across all chromosomes and populations<b>.</b> The outermost to innermost tracks are: pair-wise clustering of shared CNVs in percent showing a total of >50 Mb regions across all chromosomes in this Circos image. b) A phylogenetic tree based on the CNVs in the genome. Nei's distance between any two populations was calculated based on the CN frequencies of 379 CNV regions. Phylogenetic tree was constructed based on the neighbor-joining method; Taiwan and China are closer to each other compared to the other populations.</p

Research paper thumbnail of An understanding of spinocerebellar ataxia

Indian Journal of Medical Research, 2015

Research paper thumbnail of Association of recombination errors and young mother age in risk of Down Syndrome in South Indian population

International Journal of Advanced Research, 2016

Research paper thumbnail of RESEARCH ARTICLE Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes

☯ These authors contributed equally to this work.

Research paper thumbnail of An insight into the understanding of 5-HTR2A variants leading to schizophrenia

The Indian Journal of Medical Research, 2014

Schizophrenia is one of the most important mental disorders which is characterized by a deep disr... more Schizophrenia is one of the most important mental disorders which is characterized by a deep disruption of the thinking process and of emotional response1. It is a disabling group of brain disorders that has symptoms of hallucinations, delusions, disorganized communication, poor planning, reduced motivation and blunted affect2. The incidence of schizophrenia is relatively low (median value 15.2 per 100,000/year) and is one of the major contributors to the global burden of disease2,3. In India, the prevalence of schizophrenia is estimated to be about 3/1000 individuals4,5. Advances in genetics of schizophrenia research have established the significance of genes in aetiology, but have not identified the main relationship between observed genetic risks and specific DNA variants, protein alterations or biological processes6.

Research paper thumbnail of CNV map and phylogenetic tree

Research paper thumbnail of Identification of Potential Probiotics in the Midgut of Mulberry Silkworm, Bombyx mori Through Metagenomic Approach

Probiotics and Antimicrobial Proteins

Microorganisms play an important role in the growth and development of numerous insect species. T... more Microorganisms play an important role in the growth and development of numerous insect species. The mulberry silkworm, Bombyx mori (Lepidoptera), harbors several bacteria in its midgut aiding the metabolic processes; however, the variability of bacterial spp. present in the midgut and their role(s) in the growth and development of the silkworm are poorly understood. The present work compares the diversity of midgut bacterial communities in silkworms of variable voltinism (Pure Mysore, PM: multivoltine; CSR2: bivoltine and PM × CSR2: crossbreed) through metagenomics. The predominance of Enterococcus (30.30%) followed by Bacillus (16.96%) was observed in PM, whereas Lactobacillus (56.56%) followed by Enterococcus (10.58%) was seen only in CSR2. Interestingly, crossbreed midgut harbored diverse bacterial communities (36.21% Lactobacillus, 25.94% Bacillus, 8.1% Enterococcus, and 18.37% uncultured bacteria). Metagenomic profiles indicate variability in the gut bacterial population in different kinds of silkworms influencing the physiological activities accordingly. The dominant bacteria, particularly lactobacilli, bacilli, and enterococci could be further explored for identifying the potential probiotic consortia based on a literature survey and potential involvement in nutrient absorption, disease/stress tolerance, and improved economic traits.

Research paper thumbnail of Global patterns of large copy number variations in the human genome reveal complexity in chromosome organization

Genetics research, Jan 22, 2015

Global patterns of copy number variations (CNVs) in chromosomes are required to understand the dy... more Global patterns of copy number variations (CNVs) in chromosomes are required to understand the dynamics of genome organization and complexity. For this study, analysis was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 chip and CytoScan High-Density arrays. We identified a total of 44 109 CNVs from 1715 genomes with a mean of 25 CNVs in an individual, which established the first drafts of population-specific CNV maps providing a rationale for prioritizing chromosomal regions. About 19 905 ancient CNVs were identified across all chromosomes and populations at varying frequencies. CNV count, and sometimes CNV size, contributed to the bulk CNV size of the chromosome. Population specific lengthening and shortening of chromosomal length was observed. Sex bias for CNV presence was largely dependent on ethnicity. Lower CNV inheritance rate was observed for India, compared to YRI and CEU. A total of 33 candidate CNV hotspots from 5382 copy number (CN) variable region (CNVR) ...

Research paper thumbnail of GATA4 Specific Nonsynonymous Single-Nucleotide Polymorphisms in Congenital Heart Disease Patients of Mysore, India

Genetic Testing and Molecular Biomarkers, 2011

Congenital heart disease (CHD) is the most common type of birth defect, affecting 1% of all live ... more Congenital heart disease (CHD) is the most common type of birth defect, affecting 1% of all live births. The recent exponential increase in the knowledge of medical genetics has revolutionized the understanding of CHDs during the past few decades. GATA4, a transcription factor, is involved in heart development. There are many contradictory reports on involvement of single-nucleotide polymorphisms (SNPs) of GATA4 in the manifestation of CHD. In view of this, an attempt has been made to analyze the known SNPs of GATA4 in Mysore patients with CHD. Of the 308 CHD patients recruited, 100 were screened for SNPs of GATA4 by MassARRAY, which identified 11 SNPs, of which 6 were found in both CHD cases and controls. The other 5 SNPs, c.278G&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;C (G93A), c.1207C&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;A (L403M), c.1232C&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;T (A411V), c.1295T&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;C (L432S), and c.1180C&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;G (P394A), were found only in CHD patients. Secondary structure analysis revealed that mutant proteins with the SNPs G93A, L403M, and L432S showed structural changes in their helix, sheet, and turn. Thus, these findings suggest the involvement of specific SNPs of GATA4 in the manifestation of CHD, reported for the first time in an Indian scenario. However, screening for a larger number of CHD patients would help us to establish genotype-phenotype correlation.

Research paper thumbnail of Identifying the risk of producing aneuploids using meiotic recombination genes as biomarkers: A copy number variation approach

Indian Journal of Medical Research

Research paper thumbnail of Association of RFC1 A80G gene polymorphism with advanced maternal age in risk of Down syndrome

Current Medicine Research and Practice, 2017

Research paper thumbnail of Identification of Potential Probiotics in the Midgut of Mulberry Silkworm, Bombyx mori Through Metagenomic Approach

Probiotics and Antimicrobial Proteins

Research paper thumbnail of Genotype-Phenotype analysis of NKX 2.5 Single Nucleotide Polymorphisms involved in the Congenital Heart Disease patients of Mysore, India

Research paper thumbnail of Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes

PLOS ONE, 2015

Global spectrum of CNVs is required to catalog variations to provide a high-resolution on the dyn... more Global spectrum of CNVs is required to catalog variations to provide a high-resolution on the dynamics of genome-organization and human migration. In this study, we performed genome-wide genotyping using high-resolution arrays and identified 44,109 CNVs from 1,715 genomes across 12 populations. The study unraveled the force of independent evolutionary dynamics on genome-organizational plasticity across populations. We demonstrated the use of CNV tool to study human migration and identified a second major settlement establishing new migration routes in addition to existing ones.

Research paper thumbnail of An insight into the understanding of 5-HTR2A variants leading to schizophrenia

The Indian journal of medical research, 2014

Research paper thumbnail of Insertion-deletions burden in copy number polymorphisms of the Tibetan population

Indian Journal of Human Genetics, 2014

Many studies have been conducted to identify either insertions-deletions (inDels) or copy number ... more Many studies have been conducted to identify either insertions-deletions (inDels) or copy number variations (CNVs) in humans, but few studies have been conducted to identify both of these forms coexisting in the same region. To map the functionally significant sites within human genes that are likely to influence human traits and diseases. In this report, we describe an inDel map in the 1051 Tibetan CNV regions obtained through CNV genotyping using Affymetrix Genome-wide single nucleotide polymorphism 6.0 chip. InDel polymorphisms in these copy number polymorphism regions were identified with a computational approach using the 2500 deoxyribonucleic acid sequences obtained from the 1000 Genome Project. The study identified a total of 95935 inDels that range from 1 bp to several bps in length which were found scattered across regulatory regions, exons and in introns of genes underlying the CNVs. A study on the distribution of inDels revealed that the majority of inDels were found in coding regions of the genome than the noncoding, while within the genes, inDels in intron regions were more followed by exonic regions and finally the regulatory regions. Study of inDels in CNV regions contribute to the enhanced understanding of the role played by the two variations and their collective influence on the genome. Further, a collection of these inDel genetic markers will aid in genetic mapping, further understanding of the phenotypic variability, identification of disease genes and in detecting novel CNVs.

Research paper thumbnail of Impact of copy number variations burden on coding genome in humans using integrated high resolution arrays

Genetics research, 2014

Summary Copy number variations (CNVs) alter the transcriptional and translational levels of genes... more Summary Copy number variations (CNVs) alter the transcriptional and translational levels of genes by disrupting the coding structure and this burden of CNVs seems to be a significant contributor to phenotypic variations. Therefore it was necessary to assess the complexities of CNV burden on the coding genome. A total of 1715 individuals from 12 populations were used for CNV analysis in the present investigation. Analysis was performed using Affymetrix Genome-Wide Human SNP Array 6·0 chip and CytoScan High-Density arrays. CNVs were more frequently observed in the coding region than in the non-coding region. CNVs were observed vastly more frequently in the coding region than the non-coding region. CNVs were found to be enriched in the regions containing functional genes (83-96%) compared with the regions containing pseudogenes (4-17%). CNVs across the genome of an individual showed multiple hits across many genes, whose proteins interact physically and function under the same pathway....

Research paper thumbnail of Analysis of genetic variability among bivoltine and multivoltine silkworm genotypes using inter simple sequence repeat and simple sequence repeat markers

Research paper thumbnail of An insight into the understanding of 5-HTR2A variants leading to schizophrenia

PubMed, Dec 1, 2014

Schizophrenia is one of the most important mental disorders which is characterized by a deep disr... more Schizophrenia is one of the most important mental disorders which is characterized by a deep disruption of the thinking process and of emotional response1. It is a disabling group of brain disorders that has symptoms of hallucinations, delusions, disorganized communication, poor planning, reduced motivation and blunted affect2. The incidence of schizophrenia is relatively low (median value 15.2 per 100,000/year) and is one of the major contributors to the global burden of disease2,3. In India, the prevalence of schizophrenia is estimated to be about 3/1000 individuals4,5. Advances in genetics of schizophrenia research have established the significance of genes in aetiology, but have not identified the main relationship between observed genetic risks and specific DNA variants, protein alterations or biological processes6.

Research paper thumbnail of Identifying the risk of producing aneuploids using meiotic recombination genes as biomarkers: A copy number variation approach

Indian Journal of Medical Research, 2017

Background & objectives: Aneuploids are the most common chromosomal abnormality in liveborns and ... more Background & objectives: Aneuploids are the most common chromosomal abnormality in liveborns and are usually the result of non-disjunction (NDJ) in meiosis. Copy number variations (CNVs) are large structural variations affecting the human genome. CNVs influence critical genes involved in causing NDJ by altering their copy number which affects the clinical outcome. In this study influence of CNVs on critical meiotic recombination was examined using new computational technologies to assess their role in causing aneuploidy. Methods: This investigation was based on the analysis of 12 random normal populations consisting of 1714 individuals for aneuploid causing genes under CNV effect. To examine the effect of CNVs on genes causing aneuploidy, meiotic recombination genes were analyzed using EnrichR, WebGestalt and Ingenuity Pathway Analysis (IPA). Results: Forty three NDJ genes were found under CNV burden; IPA (Ingenuity Pathway Analysis) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis of CNV in meiotic recombination genes revealed a significant role of breast cancer gene 1, amyloid protein precursor, mitogen-activated protein kinase and nerve growth factor as key molecular players involved in causing aneuploidy. Interaction between these genes with other CNV-overlapping genes involved in cell cycle, recombination and meiosis might lead to increased incidences of aneuploidy. Interpretation & conclusions: The findings of this study implied that the effect of CNVs on normal genome contributed in amplifying the occurrences of chromosomal aneuploidies. The normal individuals consisting of variations in the susceptible genes causing aneuploids in the population remain undetected until the disorder genes express in the succeeding generations.

Research paper thumbnail of CNV map and phylogenetic tree

PLOS ONE, Apr 24, 2015

<p>a) CNV map of 379 shared CNVs across all chromosomes and populations<b>.</b>... more <p>a) CNV map of 379 shared CNVs across all chromosomes and populations<b>.</b> The outermost to innermost tracks are: pair-wise clustering of shared CNVs in percent showing a total of >50 Mb regions across all chromosomes in this Circos image. b) A phylogenetic tree based on the CNVs in the genome. Nei's distance between any two populations was calculated based on the CN frequencies of 379 CNV regions. Phylogenetic tree was constructed based on the neighbor-joining method; Taiwan and China are closer to each other compared to the other populations.</p

Research paper thumbnail of An understanding of spinocerebellar ataxia

Indian Journal of Medical Research, 2015

Research paper thumbnail of Association of recombination errors and young mother age in risk of Down Syndrome in South Indian population

International Journal of Advanced Research, 2016

Research paper thumbnail of RESEARCH ARTICLE Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes

☯ These authors contributed equally to this work.

Research paper thumbnail of An insight into the understanding of 5-HTR2A variants leading to schizophrenia

The Indian Journal of Medical Research, 2014

Schizophrenia is one of the most important mental disorders which is characterized by a deep disr... more Schizophrenia is one of the most important mental disorders which is characterized by a deep disruption of the thinking process and of emotional response1. It is a disabling group of brain disorders that has symptoms of hallucinations, delusions, disorganized communication, poor planning, reduced motivation and blunted affect2. The incidence of schizophrenia is relatively low (median value 15.2 per 100,000/year) and is one of the major contributors to the global burden of disease2,3. In India, the prevalence of schizophrenia is estimated to be about 3/1000 individuals4,5. Advances in genetics of schizophrenia research have established the significance of genes in aetiology, but have not identified the main relationship between observed genetic risks and specific DNA variants, protein alterations or biological processes6.

Research paper thumbnail of CNV map and phylogenetic tree

Research paper thumbnail of Identification of Potential Probiotics in the Midgut of Mulberry Silkworm, Bombyx mori Through Metagenomic Approach

Probiotics and Antimicrobial Proteins

Microorganisms play an important role in the growth and development of numerous insect species. T... more Microorganisms play an important role in the growth and development of numerous insect species. The mulberry silkworm, Bombyx mori (Lepidoptera), harbors several bacteria in its midgut aiding the metabolic processes; however, the variability of bacterial spp. present in the midgut and their role(s) in the growth and development of the silkworm are poorly understood. The present work compares the diversity of midgut bacterial communities in silkworms of variable voltinism (Pure Mysore, PM: multivoltine; CSR2: bivoltine and PM × CSR2: crossbreed) through metagenomics. The predominance of Enterococcus (30.30%) followed by Bacillus (16.96%) was observed in PM, whereas Lactobacillus (56.56%) followed by Enterococcus (10.58%) was seen only in CSR2. Interestingly, crossbreed midgut harbored diverse bacterial communities (36.21% Lactobacillus, 25.94% Bacillus, 8.1% Enterococcus, and 18.37% uncultured bacteria). Metagenomic profiles indicate variability in the gut bacterial population in different kinds of silkworms influencing the physiological activities accordingly. The dominant bacteria, particularly lactobacilli, bacilli, and enterococci could be further explored for identifying the potential probiotic consortia based on a literature survey and potential involvement in nutrient absorption, disease/stress tolerance, and improved economic traits.

Research paper thumbnail of Global patterns of large copy number variations in the human genome reveal complexity in chromosome organization

Genetics research, Jan 22, 2015

Global patterns of copy number variations (CNVs) in chromosomes are required to understand the dy... more Global patterns of copy number variations (CNVs) in chromosomes are required to understand the dynamics of genome organization and complexity. For this study, analysis was performed using the Affymetrix Genome-Wide Human SNP Array 6.0 chip and CytoScan High-Density arrays. We identified a total of 44 109 CNVs from 1715 genomes with a mean of 25 CNVs in an individual, which established the first drafts of population-specific CNV maps providing a rationale for prioritizing chromosomal regions. About 19 905 ancient CNVs were identified across all chromosomes and populations at varying frequencies. CNV count, and sometimes CNV size, contributed to the bulk CNV size of the chromosome. Population specific lengthening and shortening of chromosomal length was observed. Sex bias for CNV presence was largely dependent on ethnicity. Lower CNV inheritance rate was observed for India, compared to YRI and CEU. A total of 33 candidate CNV hotspots from 5382 copy number (CN) variable region (CNVR) ...

Research paper thumbnail of GATA4 Specific Nonsynonymous Single-Nucleotide Polymorphisms in Congenital Heart Disease Patients of Mysore, India

Genetic Testing and Molecular Biomarkers, 2011

Congenital heart disease (CHD) is the most common type of birth defect, affecting 1% of all live ... more Congenital heart disease (CHD) is the most common type of birth defect, affecting 1% of all live births. The recent exponential increase in the knowledge of medical genetics has revolutionized the understanding of CHDs during the past few decades. GATA4, a transcription factor, is involved in heart development. There are many contradictory reports on involvement of single-nucleotide polymorphisms (SNPs) of GATA4 in the manifestation of CHD. In view of this, an attempt has been made to analyze the known SNPs of GATA4 in Mysore patients with CHD. Of the 308 CHD patients recruited, 100 were screened for SNPs of GATA4 by MassARRAY, which identified 11 SNPs, of which 6 were found in both CHD cases and controls. The other 5 SNPs, c.278G&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;C (G93A), c.1207C&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;A (L403M), c.1232C&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;T (A411V), c.1295T&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;C (L432S), and c.1180C&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;G (P394A), were found only in CHD patients. Secondary structure analysis revealed that mutant proteins with the SNPs G93A, L403M, and L432S showed structural changes in their helix, sheet, and turn. Thus, these findings suggest the involvement of specific SNPs of GATA4 in the manifestation of CHD, reported for the first time in an Indian scenario. However, screening for a larger number of CHD patients would help us to establish genotype-phenotype correlation.

Research paper thumbnail of Identifying the risk of producing aneuploids using meiotic recombination genes as biomarkers: A copy number variation approach

Indian Journal of Medical Research

Research paper thumbnail of Association of RFC1 A80G gene polymorphism with advanced maternal age in risk of Down syndrome

Current Medicine Research and Practice, 2017

Research paper thumbnail of Identification of Potential Probiotics in the Midgut of Mulberry Silkworm, Bombyx mori Through Metagenomic Approach

Probiotics and Antimicrobial Proteins

Research paper thumbnail of Genotype-Phenotype analysis of NKX 2.5 Single Nucleotide Polymorphisms involved in the Congenital Heart Disease patients of Mysore, India

Research paper thumbnail of Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes

PLOS ONE, 2015

Global spectrum of CNVs is required to catalog variations to provide a high-resolution on the dyn... more Global spectrum of CNVs is required to catalog variations to provide a high-resolution on the dynamics of genome-organization and human migration. In this study, we performed genome-wide genotyping using high-resolution arrays and identified 44,109 CNVs from 1,715 genomes across 12 populations. The study unraveled the force of independent evolutionary dynamics on genome-organizational plasticity across populations. We demonstrated the use of CNV tool to study human migration and identified a second major settlement establishing new migration routes in addition to existing ones.

Research paper thumbnail of An insight into the understanding of 5-HTR2A variants leading to schizophrenia

The Indian journal of medical research, 2014

Research paper thumbnail of Insertion-deletions burden in copy number polymorphisms of the Tibetan population

Indian Journal of Human Genetics, 2014

Many studies have been conducted to identify either insertions-deletions (inDels) or copy number ... more Many studies have been conducted to identify either insertions-deletions (inDels) or copy number variations (CNVs) in humans, but few studies have been conducted to identify both of these forms coexisting in the same region. To map the functionally significant sites within human genes that are likely to influence human traits and diseases. In this report, we describe an inDel map in the 1051 Tibetan CNV regions obtained through CNV genotyping using Affymetrix Genome-wide single nucleotide polymorphism 6.0 chip. InDel polymorphisms in these copy number polymorphism regions were identified with a computational approach using the 2500 deoxyribonucleic acid sequences obtained from the 1000 Genome Project. The study identified a total of 95935 inDels that range from 1 bp to several bps in length which were found scattered across regulatory regions, exons and in introns of genes underlying the CNVs. A study on the distribution of inDels revealed that the majority of inDels were found in coding regions of the genome than the noncoding, while within the genes, inDels in intron regions were more followed by exonic regions and finally the regulatory regions. Study of inDels in CNV regions contribute to the enhanced understanding of the role played by the two variations and their collective influence on the genome. Further, a collection of these inDel genetic markers will aid in genetic mapping, further understanding of the phenotypic variability, identification of disease genes and in detecting novel CNVs.

Research paper thumbnail of Impact of copy number variations burden on coding genome in humans using integrated high resolution arrays

Genetics research, 2014

Summary Copy number variations (CNVs) alter the transcriptional and translational levels of genes... more Summary Copy number variations (CNVs) alter the transcriptional and translational levels of genes by disrupting the coding structure and this burden of CNVs seems to be a significant contributor to phenotypic variations. Therefore it was necessary to assess the complexities of CNV burden on the coding genome. A total of 1715 individuals from 12 populations were used for CNV analysis in the present investigation. Analysis was performed using Affymetrix Genome-Wide Human SNP Array 6·0 chip and CytoScan High-Density arrays. CNVs were more frequently observed in the coding region than in the non-coding region. CNVs were observed vastly more frequently in the coding region than the non-coding region. CNVs were found to be enriched in the regions containing functional genes (83-96%) compared with the regions containing pseudogenes (4-17%). CNVs across the genome of an individual showed multiple hits across many genes, whose proteins interact physically and function under the same pathway....