This certificate verifies that Victor Maestre Ramirez successfully completed and passed the HarvardX online course PH525.8x: Case study: DNA methylation data analysis. The course was offered through Harvard University's online learning initiative HarvardX on edX. The certificate can be verified online at the listed URL to confirm its authenticity.
Rare diseases in children and genetic diagnosis - part 1 [Today's paper]HeonjongHan
Today's paper is a review for genetic diagnosis of paediatric rare diseases.
The title is "Paediatric genomics: diagnosing rare disease in children." published in 2018, Nature review genetics.
Thanks for watching!
doi: 10.1038/nrg.2017.116.
Rare diseases in children and genetic diagnosis - part 1 [Today's paper]HeonjongHan
Today's paper is a review for genetic diagnosis of paediatric rare diseases.
The title is "Paediatric genomics: diagnosing rare disease in children." published in 2018, Nature review genetics.
Thanks for watching!
doi: 10.1038/nrg.2017.116.
Clinical Validation of Copy Number Variants Using the AMP GuidelinesGolden Helix
The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the coverage profile stored in the BAM file, which allows you to utilize your existing NGS data and perform the analysis all in one suite. Coupled with this innovative feature is the ability to annotate CNV events against a variety of databases, and by incorporating our VSClinical AMP workflow, we can now assess CNVs as potential biomarkers. Most importantly, Golden Helix CancerKB is an AMP workflow feature that provides expert-curated biomarker interpretations, including those for common somatic CNVs, that will streamline the analysis time and report generation.
In this demonstration we will cover:
Setting up the VS-CNV caller using BAM files from whole exome data
Filtering down to high quality, high confidence CNV events
Annotating CNVs using publicly curated catalogs and databases
Adding clinically relevant CNVs to the VSClinical AMP workflow
Utilizing Golden Helix CancerKB to obtain expert-curated interpretations
Showing updated features and polishes to the software
Together, VarSeq incorporates the ability to accurately call and annotate CNVs and evaluate germline and somatic mutations according to the ACMG and AMP guidelines, respectively. This webcast demonstration will provide insight into these best practice workflows and will hopefully show you how you can implement this top-quality software into your pipeline solution.
Clinical Validation of Copy Number Variant Detection by Next-Generation Seque...Golden Helix
Despite the great advances achieved in clinical genetics thanks to the incorporation of NGS (Next Generation Sequencing), a significant percentage of patients with diseases of genetic origin still do not have a conclusive molecular diagnosis. The incorporation of state-of-the-art bioinformatic methods has allowed the implementation of CNVs (Copy Number Variants) detection in NGS analysis, improving its diagnostic efficiency. In this study, the clinical utility of the detection of CNVs by NGS has been proven.
During 2018, 275 patients were studied using the NGS technique without obtaining an accurate genetic diagnosis. Bioinformatic tools that compare the normalized sequencing depth between patients and controls were used to determine CNVs. The results obtained were compared with patients own laboratory database and controls to rule out polymorphisms and false positives. All causal CNVs were confirmed by MLPA.
Pathogenic CNVs causing the disease were detected in 11 of the 275 patients (4%). Specifically, CNVs were detected for pathologies with autosomal dominant inheritance patterns (TSC2, MSH2, and FBN1), as well as for genes with autosomal recessive inheritance patterns, including two homozygous deletions (KCNV2 and RDX) and one heterozygous deletion with an SNV (Single Nucleotide Variant) in the PKHD1 gene. One of the most notable cases corresponds to a patient suspected of hypomagnesemia in which two deletions were identified in compound heterozygous mutation in the TRPM6 gene.
An overview of genomic epidemiology, Canada's IRIDA project for genome-based outbreak investigation, and a breathless romp through the awesome potential of the MinION
Establishing validity, reproducibility, and utility of highly scalable geneti...Human Variome Project
Background: New technologies and increased competition have, and will continue to improve the cost-effectiveness of genetic testing, making genetic analysis more accessible to medical practices worldwide. However, challenges remain to establishing the validity of such tests. Moreover many patients harbor rare or novel variants and classification is likely to remain a bottleneck in broader deployment of genetic medicine.
Clinical Validation of Copy Number Variants Using the AMP GuidelinesGolden Helix
The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the coverage profile stored in the BAM file, which allows you to utilize your existing NGS data and perform the analysis all in one suite. Coupled with this innovative feature is the ability to annotate CNV events against a variety of databases, and by incorporating our VSClinical AMP workflow, we can now assess CNVs as potential biomarkers. Most importantly, Golden Helix CancerKB is an AMP workflow feature that provides expert-curated biomarker interpretations, including those for common somatic CNVs, that will streamline the analysis time and report generation.
In this demonstration we will cover:
Setting up the VS-CNV caller using BAM files from whole exome data
Filtering down to high quality, high confidence CNV events
Annotating CNVs using publicly curated catalogs and databases
Adding clinically relevant CNVs to the VSClinical AMP workflow
Utilizing Golden Helix CancerKB to obtain expert-curated interpretations
Showing updated features and polishes to the software
Together, VarSeq incorporates the ability to accurately call and annotate CNVs and evaluate germline and somatic mutations according to the ACMG and AMP guidelines, respectively. This webcast demonstration will provide insight into these best practice workflows and will hopefully show you how you can implement this top-quality software into your pipeline solution.
Clinical Validation of Copy Number Variant Detection by Next-Generation Seque...Golden Helix
Despite the great advances achieved in clinical genetics thanks to the incorporation of NGS (Next Generation Sequencing), a significant percentage of patients with diseases of genetic origin still do not have a conclusive molecular diagnosis. The incorporation of state-of-the-art bioinformatic methods has allowed the implementation of CNVs (Copy Number Variants) detection in NGS analysis, improving its diagnostic efficiency. In this study, the clinical utility of the detection of CNVs by NGS has been proven.
During 2018, 275 patients were studied using the NGS technique without obtaining an accurate genetic diagnosis. Bioinformatic tools that compare the normalized sequencing depth between patients and controls were used to determine CNVs. The results obtained were compared with patients own laboratory database and controls to rule out polymorphisms and false positives. All causal CNVs were confirmed by MLPA.
Pathogenic CNVs causing the disease were detected in 11 of the 275 patients (4%). Specifically, CNVs were detected for pathologies with autosomal dominant inheritance patterns (TSC2, MSH2, and FBN1), as well as for genes with autosomal recessive inheritance patterns, including two homozygous deletions (KCNV2 and RDX) and one heterozygous deletion with an SNV (Single Nucleotide Variant) in the PKHD1 gene. One of the most notable cases corresponds to a patient suspected of hypomagnesemia in which two deletions were identified in compound heterozygous mutation in the TRPM6 gene.
An overview of genomic epidemiology, Canada's IRIDA project for genome-based outbreak investigation, and a breathless romp through the awesome potential of the MinION
Establishing validity, reproducibility, and utility of highly scalable geneti...Human Variome Project
Background: New technologies and increased competition have, and will continue to improve the cost-effectiveness of genetic testing, making genetic analysis more accessible to medical practices worldwide. However, challenges remain to establishing the validity of such tests. Moreover many patients harbor rare or novel variants and classification is likely to remain a bottleneck in broader deployment of genetic medicine.
Implementing Docker Containers with Windows Server 2019
Harvard T.H. Chan School of Public Health Certificate for PH525.8x: Case study: DNA methylation data analysis
1. Professor of Biostatistics
Harvard T.H. Chan School of Public Health
Professor of Biostatistics
and Computational Biology
Dana Farber Cancer Institute
Rafael A. Irizarry
HONOR CODE CERTIFICATE Verify the authenticity of this certificate at
CERTIFICATE
HONOR CODE
Víctor Maestre Ramírez
successfully completed and received a passing grade in
PH525.8x: Case study: DNA methylation data analysis
a course of study offered by HarvardX, an online learning
initiative of Harvard University through edX.
Issued January 11, 2016 https://verify.edx.org/cert/ad4e894d05504e8ab71a670038a572d8