Genomics Terminology - Revision history

Bradley Monk at 07:22, 29 October 2020

2020-10-29T07:22:15Z

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	* [https://gnomad.broadinstitute.org '''gnomad''' (Broad Institute) homepage]		* [https://gnomad.broadinstitute.org '''gnomad''' (Broad Institute) homepage]
	* [https://console.cloud.google.com/marketplace/product/broad-institute/gnomad gnomad on Google BigQuery]		* [https://console.cloud.google.com/marketplace/product/broad-institute/gnomad gnomad on Google BigQuery]



	== proband ==		== proband ==

Bradley Monk: /* gnomad */

2020-10-29T07:21:44Z

gnomad

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	* [https://gnomad.broadinstitute.org '''gnomad''' (Broad Institute) homepage]		* [https://gnomad.broadinstitute.org '''gnomad''' (Broad Institute) homepage]
			* [https://console.cloud.google.com/marketplace/product/broad-institute/gnomad gnomad on Google BigQuery]

	== proband ==		== proband ==

Bradley Monk at 07:19, 29 October 2020

2020-10-29T07:19:43Z

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		== gnomad ==

		The '''G'''enome '''A'''ggregation '''D'''atabase ('''gnomAD''' or '''gnomad''') is a resource developed with the goal of aggregating both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community. Version 2 (v2) of the gnomad dataset (GRCh37) spans 125,748 exome sequences and 15,708 whole-genome sequences from unrelated individuals sequenced as part of various disease-specific and population genetic studies. Version 3 (v3) data set (GRCh38) spans 71,702 genomes. All data is released without restriction on use.

		* [https://gnomad.broadinstitute.org '''gnomad''' (Broad Institute) homepage]

Bradley Monk at 07:14, 29 October 2020

2020-10-29T07:14:22Z

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	A proband is an individual serving as the starting point for the genetic study of a family (used especially in medicine). A proband is usually the first affected individual in a family who brings a genetic disorder to the attention of the medical community.		A proband is an individual serving as the starting point for the genetic study of a family (used especially in medicine). A proband is usually the first affected individual in a family who brings a genetic disorder to the attention of the medical community.



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			== Hail ==

			[https://hail.is/docs/0.2/index.html Hail] is an open-source library for scalable data exploration and analysis, with a particular emphasis on genomics. See the overview for a high-level walkthrough of the library, the GWAS tutorial for a simple example of conducting a genome-wide association study, and the installation page to get started using Hail.

			* [https://hail.is/docs/0.2/index.html Hail homepage]
			* [https://github.com/danking/hail-cloud-docs/blob/master/how-to-cloud.md Hail - ''how to cloud'']



			== GATK ==

			The '''G'''enome '''A'''nalysis '''T'''ool'''K'''it (GATK) is a genomic analysis toolkit focused on variant discovery. GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope includes somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data, and bundles the popular Picard toolkit.

			These tools were primarily designed to process exomes and whole genomes generated with Illumina sequencing technology, but they can be adapted to handle a variety of other technologies and experimental designs. And although it was originally developed for human genetics, the GATK has since evolved to handle genome data from any organism, with any level of ploidy.

			* [https://gatk.broadinstitute.org/hc/en-us GATK homepage]
			* [https://gatk.broadinstitute.org/hc/en-us/community/topics GATK community topics]

Bradley Monk: /* human genome */

2020-10-29T07:00:12Z

human genome

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Bradley Monk at 06:50, 29 October 2020

2020-10-29T06:50:45Z

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	=== proband ===		== proband ==

	A proband is an individual serving as the starting point for the genetic study of a family (used especially in medicine). A proband is usually the first affected individual in a family who brings a genetic disorder to the attention of the medical community.		A proband is an individual serving as the starting point for the genetic study of a family (used especially in medicine). A proband is usually the first affected individual in a family who brings a genetic disorder to the attention of the medical community.


	=== trio analysis ===		== trio analysis ==

	A trio refers to 2 parents + 1 offspring (2 + 1 = 3, hence trio). In medical genetics, trio analysis often means the analysis of a proband's genome and along with their parents genome. An exome trio-based approach is fundamental to the identification of heterozygous dominant pathogenic variants (in an afflicted proband and their unaffected parents).		A trio refers to 2 parents + 1 offspring (2 + 1 = 3, hence trio). In medical genetics, trio analysis often means the analysis of a proband's genome and along with their parents genome. An exome trio-based approach is fundamental to the identification of heterozygous dominant pathogenic variants (in an afflicted proband and their unaffected parents).
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	=== human genome ===		== human genome ==

	The total length of the [https://en.wikipedia.org/wiki/Human_genome human genome] is over 3 billion base pairs. The genome is organized into 22 paired chromosomes, termed [https://en.wikipedia.org/wiki/autosome autosomes], plus the 23rd pair of sex chromosomes (XX) in the female, and (XY) in the male. These are all large linear DNA molecules contained within the cell nucleus. The genome also includes the mitochondrial DNA, a comparatively small circular molecule present in each mitochondrion. Basic information about these molecules and their gene content, based on a reference genome that does not represent the sequence of any specific individual, are provided in the following table.		The total length of the [https://en.wikipedia.org/wiki/Human_genome human genome] is over 3 billion base pairs. The genome is organized into 22 paired chromosomes, termed [https://en.wikipedia.org/wiki/autosome autosomes], plus the 23rd pair of sex chromosomes (XX) in the female, and (XY) in the male. These are all large linear DNA molecules contained within the cell nucleus. The genome also includes the mitochondrial DNA, a comparatively small circular molecule present in each mitochondrion. Basic information about these molecules and their gene content, based on a reference genome that does not represent the sequence of any specific individual, are provided in the following table.
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	==~~= number of~~ human genes ===		== human genes (count) ==

	'''The number of genes''' in the human genome (see: [https://en.wikipedia.org/wiki/Category:Genes_by_human_chromosome '''full gene list''']) is not entirely clear because the function of numerous transcripts remains unclear. This is especially true for non-coding RNA (see below). The number of protein-coding genes is better known but there are still on the order of 1,400 questionable genes which may or may not encode functional proteins, usually encoded by short open reading frames. Table 2 gives estimates from various projects and shows these discrepancies.		'''The number of genes''' in the human genome (see: [https://en.wikipedia.org/wiki/Category:Genes_by_human_chromosome '''full gene list''']) is not entirely clear because the function of numerous transcripts remains unclear. This is especially true for non-coding RNA (see below). The number of protein-coding genes is better known but there are still on the order of 1,400 questionable genes which may or may not encode functional proteins, usually encoded by short open reading frames. Table 2 gives estimates from various projects and shows these discrepancies.

Bradley Monk: /* human genome */

2020-10-29T06:49:48Z

human genome

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	'''Table 1''' (above) summarizes the physical organization and gene content of the human reference genome, with links to the original analysis, as published in the Ensembl database at the European Bioinformatics Institute (EBI) and Wellcome Trust Sanger Institute. Chromosome lengths were estimated by multiplying the number of base pairs by 0.34 nanometers, the distance between base pairs in the DNA double helix. A recent estimation of human chromosome lengths based on updated data reports 205.00 cm for the diploid male genome and 208.23 cm for female, corresponding to weights of 6.41 and 6.51 picograms (pg), respectively. The number of proteins is based on the number of initial precursor mRNA transcripts, and does not include products of alternative pre-mRNA splicing, or modifications to protein structure that occur after translation.		'''Table 1''' (above) summarizes the physical organization and gene content of the human reference genome, with links to the original analysis, as published in the Ensembl database at the European Bioinformatics Institute (EBI) and Wellcome Trust Sanger Institute. Chromosome lengths were estimated by multiplying the number of base pairs by 0.34 nanometers, the distance between base pairs in the DNA double helix. A recent estimation of human chromosome lengths based on updated data reports 205.00 cm for the diploid male genome and 208.23 cm for female, corresponding to weights of 6.41 and 6.51 picograms (pg), respectively. The number of proteins is based on the number of initial precursor mRNA transcripts, and does not include products of alternative pre-mRNA splicing, or modifications to protein structure that occur after translation.

	'''The number of genes''' in the human genome is not entirely clear because the function of numerous transcripts remains unclear. This is especially true for non-coding RNA (see below). The number of protein-coding genes is better known but there are still on the order of 1,400 questionable genes which may or may not encode functional proteins, usually encoded by short open reading frames. Table 2 gives estimates from various projects and shows these discrepancies.

			=== number of human genes ===

			'''The number of genes''' in the human genome (see: [https://en.wikipedia.org/wiki/Category:Genes_by_human_chromosome '''full gene list''']) is not entirely clear because the function of numerous transcripts remains unclear. This is especially true for non-coding RNA (see below). The number of protein-coding genes is better known but there are still on the order of 1,400 questionable genes which may or may not encode functional proteins, usually encoded by short open reading frames. Table 2 gives estimates from various projects and shows these discrepancies.

	{\| class="wikitable"		{\| class="wikitable"
	\|+Table 2. Number of human genes in different databases ~~as of July 2018~~		\|+Table 2. Number of human genes<br />(according to different databases)
	!		!
	!Gencode		!Gencode
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	\|328,827		\|328,827
	\|}		\|}


	Human genetic variations are unique DNA sequence differences that have been identified in the individual human genome sequences analyzed by Ensembl as of December 2016. The number of identified variations is expected to increase as further Personal genomics\|personal genomes are sequenced and analyzed. In addition to the gene content shown in this table, a large number of non-expressed functional sequences have been identified throughout the human genome (see below). Links open windows to the reference chromosome sequences in the EBI genome browser.

	Small non-coding RNAs are RNAs of as many as 200 bases that do not have protein-coding potential. These include: microRNAs, or miRNAs (post-transcriptional regulators of gene expression), small nuclear RNAs, or snRNAs (the RNA components of spliceosomes), and small nucleolar RNAs, or snoRNA (involved in guiding chemical modifications to other RNA molecules). Long non-coding RNAs are RNA molecules longer than 200 bases that do not have protein-coding potential. These include: ribosomal RNAs, or rRNAs (the RNA components of ribosomes), and a variety of other long RNAs that are involved in regulation of gene expression, epigenetic modifications of DNA nucleotides and histone proteins, and regulation of the activity of protein-coding genes. Small discrepancies between total-small-ncRNA numbers and the numbers of specific types of small ncNRAs result from the former values being sourced from Ensembl release 87 and the latter from Ensembl release 68.

	The entropy rate of the genome differs significantly between coding and non-coding sequences. It is close to the maximum of 2 bits per base pair for the coding sequences (about 45 million base pairs), but less for the non-coding parts. It ranges between 1.5 and 1.9 bits per base pair for the individual chromosome, except for the Y-chromosome, which has an entropy rate below 0.9 bits per base pair.

Bradley Monk: /* human genome */

2020-10-29T06:41:12Z

human genome

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Bradley Monk at 06:17, 29 October 2020

2020-10-29T06:17:58Z

← Older revision		Revision as of 23:17, 28 October 2020
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	== ~~Molecular organization and gene content~~ ==		=== human genome ===

	The total length of the [https://en.wikipedia.org/wiki/Human_genome human genome] is over 3 billion base pairs. The genome is organized into 22 paired chromosomes, termed [https://en.wikipedia.org/wiki/autosome autosomes], plus the 23rd pair of sex chromosomes (XX) in the female, and (XY) in the male. These are all large linear DNA molecules contained within the cell nucleus. The genome also includes the mitochondrial DNA, a comparatively small circular molecule present in each mitochondrion. Basic information about these molecules and their gene content, based on a reference genome that does not represent the sequence of any specific individual, are provided in the following table.		The total length of the [https://en.wikipedia.org/wiki/Human_genome human genome] is over 3 billion base pairs. The genome is organized into 22 paired chromosomes, termed [https://en.wikipedia.org/wiki/autosome autosomes], plus the 23rd pair of sex chromosomes (XX) in the female, and (XY) in the male. These are all large linear DNA molecules contained within the cell nucleus. The genome also includes the mitochondrial DNA, a comparatively small circular molecule present in each mitochondrion. Basic information about these molecules and their gene content, based on a reference genome that does not represent the sequence of any specific individual, are provided in the following table.

Bradley Monk: /* Molecular organization and gene content */

2020-10-29T06:17:14Z

Molecular organization and gene content

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