Cover: In Spector and Wiita. (http://doi.org/10.1002/cphg.106), the image shows a screenshot of ClinTAD's Single page for the example case. The top section of this page contains the input fields. The middle section contains an interactive visualization with several types of elements. These elements can include topologically associated domains (red), the copy number variant (green), genes with no phenotype matches (blue), genes with phenotype matches (orange), VISTA enhancers (purple), and DGV duplications (blue) and deletions (red). For the example case, both the MCTP2 (left side) and NR2F2 ..read more

Abstract Novel cytogenetic tools are increasingly based on genome sequencing for detecting chromosomal abnormalities. Different sequence‐based techniques optimized for diagnosis of structural variants can be useful for narrowing down the localization of breakpoints of chromosomal abnormalities, but do not offer nucleotide resolution of breakpoints for proper interpretation of gene disruption. This protocol presents the characterization of structural variants at nucleotide resolution using Sanger sequencing after low‐pass large‐insert genome sequencing or other long‐molecule methods. © 2020 Wil ..read more

Abstract Genetic research often utilizes or generates information that is potentially sensitive to individuals, families, or communities. For these reasons, genetic research may warrant additional scrutiny from investigators and governmental regulators, compared to other types of biomedical research. The informed consent process should address the range of social and psychological issues that may arise in genetic research. This article addresses a number of these issues, including recruitment of participants, disclosure of results, psychological impact of results, insurance and employment disc ..read more

Abstract DNA copy number variants (CNVs) are routinely evaluated as part of clinical diagnosis in both the prenatal and postnatal genetic settings. Current guidelines for interpreting the potential clinical significance of these CNVs, typically identified by chromosomal microarray, focus entirely on genes localized within the CNV region. However, recent work has suggested that some CNVs can actually produce clinical impacts by influencing transcription of genes outside the CNV region. These alterations of transcription appear to occur by disrupting the composition of DNA topologically associat ..read more

Abstract The AD Knowledge Portal (adknowledgeportal.org) is a public data repository that shares data and other resources generated by multiple collaborative research programs focused on aging, dementia, and Alzheimer's disease (AD). In this article, we highlight how to use the Portal to discover and download genomic variant and transcriptomic data from the same individuals. First, we show how to use the web interface to browse and search for data of interest using relevant file annotations. We demonstrate how to learn more about the context surrounding the data, including diagnostic criteria ..read more

Cover: In Spector and Wiita. (http://doi.org/10.1002/cphg.106), the image shows a screenshot of ClinTAD's Single page for the example case. The top section of this page contains the input fields. The middle section contains an interactive visualization with several types of elements. These elements can include topologically associated domains (red), the copy number variant (green), genes with no phenotype matches (blue), genes with phenotype matches (orange), VISTA enhancers (purple), and DGV duplications (blue) and deletions (red). For the example case, both the MCTP2 (left side) and NR2F2 ..read more

Abstract Novel cytogenetic tools are increasingly based on genome sequencing for detecting chromosomal abnormalities. Different sequence‐based techniques optimized for diagnosis of structural variants can be useful for narrowing down the localization of breakpoints of chromosomal abnormalities, but do not offer nucleotide resolution of breakpoints for proper interpretation of gene disruption. This protocol presents the characterization of structural variants at nucleotide resolution using Sanger sequencing after low‐pass large‐insert genome sequencing or other long‐molecule methods. © 2020 Wil ..read more

Abstract Genetic research often utilizes or generates information that is potentially sensitive to individuals, families, or communities. For these reasons, genetic research may warrant additional scrutiny from investigators and governmental regulators, compared to other types of biomedical research. The informed consent process should address the range of social and psychological issues that may arise in genetic research. This article addresses a number of these issues, including recruitment of participants, disclosure of results, psychological impact of results, insurance and employment disc ..read more

Abstract DNA copy number variants (CNVs) are routinely evaluated as part of clinical diagnosis in both the prenatal and postnatal genetic settings. Current guidelines for interpreting the potential clinical significance of these CNVs, typically identified by chromosomal microarray, focus entirely on genes localized within the CNV region. However, recent work has suggested that some CNVs can actually produce clinical impacts by influencing transcription of genes outside the CNV region. These alterations of transcription appear to occur by disrupting the composition of DNA topologically associat ..read more

Abstract The AD Knowledge Portal (adknowledgeportal.org) is a public data repository that shares data and other resources generated by multiple collaborative research programs focused on aging, dementia, and Alzheimer's disease (AD). In this article, we highlight how to use the Portal to discover and download genomic variant and transcriptomic data from the same individuals. First, we show how to use the web interface to browse and search for data of interest using relevant file annotations. We demonstrate how to learn more about the context surrounding the data, including diagnostic criteria ..read more