List of works - Sumit Middha

A FISH assay efficiently screens for BRAF gene rearrangements in pancreatic acinar-type neoplasms

scientific article published on 8 September 2017

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines

scientific article

Application of whole exome sequencing in undiagnosed inherited polyneuropathies.

scientific article published on 6 March 2014

Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants

scientific article

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data

scientific article

Characterizing genetic variation of adrenergic signalling pathways in Takotsubo (stress) cardiomyopathy exomes.

scientific article published on 8 August 2014

Chromosome 20q Amplification Defines a Subtype of Microsatellite Stable, Left-Sided Colon Cancers with Wild-type RAS/RAF and Better Overall Survival

scientific article published on 9 February 2017

Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells

scientific article published on 30 September 2015

Comprehensive assessment of genetic variants within TCF4 in Fuchs' endothelial corneal dystrophy

scientific article

Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression

scientific article published on 14 May 2015

Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics.

scientific article

Evolution and potential function of fibrinogen-like domains across twelve Drosophila species

scientific article

Exome Sequencing and Systems Biology Converge to Identify Novel Mutations in the L-Type Calcium Channel, CACNA1C , Linked to Autosomal Dominant Long QT Syndrome ⬇️

scientific article published on June 1, 2013

From days to hours: reporting clinically actionable variants from whole genome sequencing

scientific article

Gene Expression Signatures Characterized by Longitudinal Stability and Interindividual Variability Delineate Baseline Phenotypic Groups with Distinct Responses to Immune Stimulation

scientific article published on 19 January 2018

Gene expression patterns in CD4+ peripheral blood cells in healthy subjects and stage IV melanoma patients.

scientific article published on 06 August 2015

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

scientific article

Genetic diversity of tumors with mismatch repair deficiency influences anti-PD-1 immunotherapy response

scientific article published on 01 May 2019

Genome-wide characterization of transcriptional patterns in high and low antibody responders to rubella vaccination

scientific article

Genomic Alterations in Fatal Forms of Non-Anaplastic Thyroid Cancer: Identification of MED12 and RBM10 as Novel Thyroid Cancer Genes Associated with Tumor Virulence

scientific article published on 20 June 2017

Glutathione S-transferase omega genes in Alzheimer and Parkinson disease risk, age-at-diagnosis and brain gene expression: an association study with mechanistic implications

scientific article

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

scientific article

Histone deacetylase inhibition promotes osteoblast maturation by altering the histone H4 epigenome and reduces Akt phosphorylation.

scientific article published on 12 August 2013

Homozygous/Compound Heterozygous Triadin Mutations Associated With Autosomal-Recessive Long-QT Syndrome and Pediatric Sudden Cardiac Arrest: Elucidation of the Triadin Knockout Syndrome.

scientific article published on 28 April 2015

How well do whole exome sequencing results correlate with medical findings? A study of 89 Mayo Clinic Biobank samples

scientific article published on 24 July 2015

Identification and characterization of a novel promoter for the human ANO1 gene regulated by the transcription factor signal transducer and activator of transcription 6 (STAT6)

scientific article

Identification of Targetable Kinase Alterations in Patients with Colorectal Carcinoma That are Preferentially Associated with Wild-Type RAS/RAF

scientific article published on 11 December 2015

Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set

scientific article

Identification of novel variants in colorectal cancer families by high-throughput exome sequencing

scientific article published on May 2013

Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma

scientific article

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

scientific article

Mitochondrial Aging and Physical Decline: Insights From Three Generations of Women

scientific article

Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues

scientific article

Mutational landscape of candidate genes in familial prostate cancer

scientific article

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.

scientific article published on 8 May 2017

Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss

scientific article

New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice

scientific article

Novel High-grade Endometrial Stromal Sarcoma: A Morphologic Mimicker of Myxoid Leiomyosarcoma

scientific article published on 14 September 2016

Novel SOD1 mutation discovered in atypical ALS by whole exome sequencing ⬇️

scientific article published on June 6, 2013

Novel TRAF1-ALK fusion identified by deep RNA sequencing of anaplastic large cell lymphoma

scientific article published on 02 September 2013

Novel late-onset Alzheimer disease loci variants associate with brain gene expression

scientific article

Novel splice site mutations in the gamma glutamyl carboxylase gene in a child with congenital combined deficiency of the vitamin K-dependent coagulation factors (VKCFD).

scientific article published in July 2009

Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience

scientific article published on 02 September 2016

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

scientific article published on 21 September 2016

Recurrent, truncating SOX9 mutations are associated with SOX9 overexpression, KRAS mutation, and TP53 wild type status in colorectal carcinoma.

scientific article published on 29 May 2016

Reliable Detection of Mismatch Repair Deficiency in Colorectal Cancers Using Mutational Load in Next-Generation Sequencing Panels

scientific article published on 28 March 2016

Reliable Pan-Cancer Microsatellite Instability Assessment by Using Targeted Next-Generation Sequencing Data

scientific article published on 03 October 2017

Retained mismatch repair protein expression occurs in approximately 6% of microsatellite instability-high cancers and is associated with missense mutations in mismatch repair genes

scientific article published on 19 December 2019

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

scientific article published on 10 June 2012

Somatic HNF1A mutations in the malignant transformation of hepatocellular adenomas: a retrospective analysis of data from MSK-IMPACT and TCGA

scientific article published on 17 August 2018

TNNI3K mutation in familial syndrome of conduction system disease, atrial tachyarrhythmia and dilated cardiomyopathy

scientific article

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

scientific article (publication date: 15 January 2012)

The genetic landscape of endometrial clear cell carcinomas.

scientific article published on 18 July 2017

The human gut microbiome: current knowledge, challenges, and future directions

scientific article

Universal screening for microsatellite instability in colorectal cancer in the clinical genomics era: new recommendations, methods, and considerations

scientific article published on 01 October 2017

Whole exome sequencing in 75 high-risk families with validation and replication in independent case-control studies identifies TANGO2, OR5H14, and CHAD as new prostate cancer susceptibility genes

scientific article

Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements

scientific article

Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides

scientific article

List of works by Sumit Middha

A FISH assay efficiently screens for BRAF gene rearrangements in pancreatic acinar-type neoplasms

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines

Application of whole exome sequencing in undiagnosed inherited polyneuropathies.

Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data

Characterizing genetic variation of adrenergic signalling pathways in Takotsubo (stress) cardiomyopathy exomes.

Chromosome 20q Amplification Defines a Subtype of Microsatellite Stable, Left-Sided Colon Cancers with Wild-type RAS/RAF and Better Overall Survival

Comparison of the Life Cycles of Genetically Distant Species C and Species D Human Adenoviruses Ad6 and Ad26 in Human Cells

Comprehensive assessment of genetic variants within TCF4 in Fuchs' endothelial corneal dystrophy

Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression

Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics.

Evolution and potential function of fibrinogen-like domains across twelve Drosophila species

Exome Sequencing and Systems Biology Converge to Identify Novel Mutations in the L-Type Calcium Channel, CACNA1C , Linked to Autosomal Dominant Long QT Syndrome ⬇️

From days to hours: reporting clinically actionable variants from whole genome sequencing

Gene Expression Signatures Characterized by Longitudinal Stability and Interindividual Variability Delineate Baseline Phenotypic Groups with Distinct Responses to Immune Stimulation

Gene expression patterns in CD4+ peripheral blood cells in healthy subjects and stage IV melanoma patients.

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

Genetic diversity of tumors with mismatch repair deficiency influences anti-PD-1 immunotherapy response

Genome-wide characterization of transcriptional patterns in high and low antibody responders to rubella vaccination

Genomic Alterations in Fatal Forms of Non-Anaplastic Thyroid Cancer: Identification of MED12 and RBM10 as Novel Thyroid Cancer Genes Associated with Tumor Virulence

Glutathione S-transferase omega genes in Alzheimer and Parkinson disease risk, age-at-diagnosis and brain gene expression: an association study with mechanistic implications

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data

Histone deacetylase inhibition promotes osteoblast maturation by altering the histone H4 epigenome and reduces Akt phosphorylation.

Homozygous/Compound Heterozygous Triadin Mutations Associated With Autosomal-Recessive Long-QT Syndrome and Pediatric Sudden Cardiac Arrest: Elucidation of the Triadin Knockout Syndrome.

How well do whole exome sequencing results correlate with medical findings? A study of 89 Mayo Clinic Biobank samples

Identification and characterization of a novel promoter for the human ANO1 gene regulated by the transcription factor signal transducer and activator of transcription 6 (STAT6)

Identification of Targetable Kinase Alterations in Patients with Colorectal Carcinoma That are Preferentially Associated with Wild-Type RAS/RAF

Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set

Identification of novel variants in colorectal cancer families by high-throughput exome sequencing

Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

Mitochondrial Aging and Physical Decline: Insights From Three Generations of Women

Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues

Mutational landscape of candidate genes in familial prostate cancer

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.

Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss

New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice

Novel High-grade Endometrial Stromal Sarcoma: A Morphologic Mimicker of Myxoid Leiomyosarcoma

Novel SOD1 mutation discovered in atypical ALS by whole exome sequencing ⬇️

Novel TRAF1-ALK fusion identified by deep RNA sequencing of anaplastic large cell lymphoma

Novel late-onset Alzheimer disease loci variants associate with brain gene expression

Novel splice site mutations in the gamma glutamyl carboxylase gene in a child with congenital combined deficiency of the vitamin K-dependent coagulation factors (VKCFD).

Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

Recurrent, truncating SOX9 mutations are associated with SOX9 overexpression, KRAS mutation, and TP53 wild type status in colorectal carcinoma.

Reliable Detection of Mismatch Repair Deficiency in Colorectal Cancers Using Mutational Load in Next-Generation Sequencing Panels

Reliable Pan-Cancer Microsatellite Instability Assessment by Using Targeted Next-Generation Sequencing Data

Retained mismatch repair protein expression occurs in approximately 6% of microsatellite instability-high cancers and is associated with missense mutations in mismatch repair genes

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Somatic HNF1A mutations in the malignant transformation of hepatocellular adenomas: a retrospective analysis of data from MSK-IMPACT and TCGA

TNNI3K mutation in familial syndrome of conduction system disease, atrial tachyarrhythmia and dilated cardiomyopathy

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

The genetic landscape of endometrial clear cell carcinomas.

The human gut microbiome: current knowledge, challenges, and future directions

Universal screening for microsatellite instability in colorectal cancer in the clinical genomics era: new recommendations, methods, and considerations

Whole exome sequencing in 75 high-risk families with validation and replication in independent case-control studies identifies TANGO2, OR5H14, and CHAD as new prostate cancer susceptibility genes

Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements

Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides