GRCz11 – the latest zebrafish reference genome assembly
After 2.5 years of assembly curation, the GRC is proud to present the new zebrafish reference genome assembly,GRCz11.This latest assembly has been refined by the addition of nearly 1000 finished clone sequences and by the resolution of more than 400 assembly issues. This resulted in a significant reduction in scaffold numbers (3399 to 1905) and increase in scaffold N50 (2.18 Mb to 7.5 Mb) whilst the overall genome size was not affected. Figure 1 shows an overview of contig and scaffold N50s over time, indicating the advance in assembly curation.Figure 1: Contig vs. scaffold N50s for zebrafish reference genome assembli...
Source: GenomeRef - May 23, 2017 Category: Genetics & Stem Cells Source Type: blogs
New haplotype representations in the LRC_KIR region on chromosome 19q13.4
The KIR (Killer cell immunoglobulin-like receptor) gene cluster is a region of approximately 150 kb within the Leukocyte Receptor Complex (LRC) on human chromosome 19q13.4 (CM000681.2: 50900001-58617616). The KIR family is highly divergent, with multiple haplotypes differing in gene content, and with individual genes exhibiting allelic variation. Only a few KIR genes are conserved between humans and chimpanzees, the closest living relatives to humans. The GRCh38 assembly includes 35 representations for the LRC-KIR region as alternate loci scaffolds in addition to the chromosomal sequence (ALT_REF_LOCI in LRC-KIR region). D...
Source: GenomeRef - November 8, 2016 Category: Genetics & Stem Cells Source Type: blogs
Are you familiar with CYP2D6 and its importance in drug metabolism?
CYP2D6 (Gene ID: 1565) is a gene associated with the metabolism of ~25% of clinically prescribed drugs, including antidepressants, neuroleptics and opioids. CYP2D6 is located onchromosome 22 (22q13.1), near two cytochrome P450 pseudogenesCYP2D7 andCYP2D8P. Because of its functional importance, the GRC updated the chromosomal representation for CYP2D6 to the sequence-corrected clinical standard (CYP2D6*1A) in GRCh38. The version of CYP2D6 found in the prior assembly version, GRCh37, was retained in GRCh38 as an alternate loci scaffold (KI270928.1).The Genome Reference Consortium, in conjunction with thePharmacogen...
Source: GenomeRef - October 24, 2016 Category: Genetics & Stem Cells Source Type: blogs
Are you familiar with CYP2D6 and it's importance in drug metabolism?
CYP2D6 (Gene ID: 1565) is a gene associated with the metabolism of ~25% of clinically prescribed drugs, including antidepressants, neuroleptics and opioids. CYP2D6 is located onchromosome 22 (22q13.1), near two cytochrome P450 pseudogenesCYP2D7 andCYP2D8P. Because of its functional importance, the GRC updated the chromosomal representation for CYP2D6 to the sequence-corrected clinical standard (CYP2D6*1A) in GRCh38. The version of CYP2D6 found in the prior assembly version, GRCh37, was retained in GRCh38 as an alternate loci scaffold (KI270928.1).The Genome Reference Consortium, in conjunction with thePharmacogen...
Source: GenomeRef - October 24, 2016 Category: Genetics & Stem Cells Source Type: blogs
ZFIN joins the GRC
ZFIN, the zebrafish model organism database, is joining the GRC and is planning to take over the maintenance and curation of the zebrafish genome assembly. ZFIN curators visited with GRC curators at the Wellcome Trust Sanger Institute in January 2016 to undergo training in the use of GRC tools and processes. ZFIN anticipates taking over responsibility after the next planned release of the zebrafish assembly, GRCz11. A specific timeline for this release has not yet been established, but is likely to be towards the end of 2016. ZFIN curators will continue training through 2016 with GRC curators on zebrafish genome issues.ZFI...
Source: GenomeRef - May 17, 2016 Category: Genetics & Stem Cells Source Type: blogs
Chicken assembly curation at GRC
Upon the release of Gallus_gallus-5.0 (GCA_000002315.3), the GRC assumed responsibility for the continued curation of the chicken reference genome assembly from the International Chicken Genome Consortium. The assembly represents the Red Jungle Fowl strain, inbred line UCD001. All sequences in the assembly are derived from a single individual from this line, female "RJF #256". The assembly is a hybrid comprised primarily of WGS contigs, into which genomic clones have been integrated. Planned curation efforts are focused on selecting genomic clones (BACs) for sequencing and assembly, specifically from the CHORI-261 library,...
Source: GenomeRef - April 18, 2016 Category: Genetics & Stem Cells Source Type: blogs
Updates to DUX4 region on subtelomeric chromosome 4q
Sequence improvements and increased variant representation in the human genome reference assembly are priorities for the GRC. This blog post describes two updates in the recent GRCh38.p7 patch release affecting the DUX4 region located at the chromosome 4q sub-telomere: (1) a FIX patch correcting the chromosomal representation (KQ983257.1) and (2) a NOVEL patch representing a variant of the region (KQ983258.1). A third haplotype of DUX4 region which is represented in GRCh37 will be also described.The DUX4 region contains tandem arrays of a 3.3 Kb D4Z4 macrosatellite repeat located in the sub-telomer...
Source: GenomeRef - April 7, 2016 Category: Genetics & Stem Cells Source Type: blogs
GRC reference assembly curation with BioNano maps
Commercial whole genome mapping systems, such as OpGen and BioNano, are playing an increasingly important role in a variety of genomic analyses, including de novo assembly, structural variant detection and assembly curation.Comparison of a reference assembly to a collection of whole genome maps can help curators find potential regions of misassembly and identify genomic variations that are candidates for representation in alternate loci scaffolds. For example, optical maps played a key role in the GRC's resolution of the human 10q11.22 tiling path, as described in this prior GRC blog post.To assist with curation efforts, t...
Source: GenomeRef - March 9, 2016 Category: Genetics & Stem Cells Source Type: blogs
GRC Website: Individual Genome Issues
Are you looking for the latest status updates from the GRC on the human, mouse or zebrafish reference genome assemblies? In companion to our previous post, we now explain how to use the Individual Genome Issue reports on the GRC website. As described in our last blog, you can filter and search for issues of interest using the organism-specific "Issues Under Review" pages. To provide an example for this blog post, we applied the follow filtering options on the human "Issues Under Review" page: issues location = GRCh38.p2, chromosome = chr3 , type = variation and scaffol...
Source: GenomeRef - February 19, 2015 Category: Genetics & Stem Cells Source Type: blogs
GRC Website Update: Genome Issues Under Review
GRC "Genome Issues under Review" webpage update!Do you know how to find genome issues on the GRC website? To get started, select an organism from the top of the GRC homepage, and in the corresponding organism overview page select the link for "Issues Under Review". These pages provide you with the latest information about potential problems and other issues related to the human, mouse and zebrafish reference genome assemblies that the GRC are working on. Recent updates to these pages make them more interactive, informative and easier to navigate so you can pinpoint issues relevant to your research inter...
Source: GenomeRef - February 3, 2015 Category: Genetics & Stem Cells Source Type: blogs
GRCh38: Patching the ABO gene
GRCh38 has started receiving patch updates, and this blog post describes a FIX patch to the ABO gene, located on chr. 9. You might have been aware that the GRC released a FIX patch to ABO for GRCh37. So why is there an ABO FIX patch for GRCh38 as well?In GRCh37, the ABO gene was annotated on sequence derived from two RP11 library clones, AL732364.9 (RP11-244N20) and AL158826.23 (RP11-430N14). However, the RP11 library is derived from a diploid genome and analysis demonstrated that the two sequenced clones represented two different Type O ABO alleles. As a result, the GRCh37 chr.9 representation of ABO was an invalid ...
Source: GenomeRef - January 28, 2015 Category: Genetics & Stem Cells Source Type: blogs
Optical Mapping data in the GRC track hub
The GRC track hub now includes Optical Mapping analysis information.What is Optical Mapping? Optical Mapping (OM) is a method to produce ordered restriction maps from single DNA molecules (rMaps). These rMaps are assembled into consensus maps which can be aligned against the reference assembly, taking into account the positioning of restriction sites and length of fragments. OM aids the scaffolding of genomic sequence and the identification of errors in genome assemblies, but it is also very helpful in confirming assembled contigs and sizing gaps.What OM data is available?OM data is currently available for human (T...
Source: GenomeRef - November 27, 2014 Category: Genetics & Stem Cells Source Type: blogs
GRC track hub arrives!
The GRC are now providing assembly-related tracks for reference genomes via a track hub, which will allow you to view that data in a range of genome browsers, including Ensembl and UCSC. The location of this hub is: http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txtWhat tracks are available?The GRC generates a range of annotations on the reference genomes it curates. These tracks describe the assembly of the genome, as well as quality issues with the genome, and provides information relevant to their resolution or planned improvement. Much of this annotation is already available via the gEVAL browse...
Source: GenomeRef - October 21, 2014 Category: Genetics & Stem Cells Source Type: blogs
GRCh38.p1 has arrived!
The first patch release for the GRCh38 reference assembly is now available. The GRCh38.p1 release includes 16 scaffolds: 13 FIX patches and 3 NOVEL patches. The FIX patch scaffolds correct existing assembly sequences, while the NOVEL patch scaffolds provide new alternate sequence representations. You can download the GRCh38.p1 assembly, including the alignments of the patches to GRCh38, from the GenBank FTP site: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.16_GRCh38.p1/.Stay tuned for upcoming blog posts on individual patches! (Source: GenomeRef)
Source: GenomeRef - October 14, 2014 Category: Genetics & Stem Cells Source Type: blogs
GRCz10 - The GRC's first zebrafish genome reference assembly
< div dir= " ltr " style= " text-align: left; " trbidi= " on " > < a href= " http://1.bp.blogspot.com/-9b56Lw1vwbE/VA8KWJLR8mI/AAAAAAAAAIY/bVykULGeW5k/s1600/image.jpeg " imageanchor= " 1 " style= " clear: right; float: right; margin-bottom: 1em; margin-left: 1em; " > < img border= " 0 " src= " http://1.bp.blogspot.com/-9b56Lw1vwbE/VA8KWJLR8mI/AAAAAAAAAIY/bVykULGeW5k/s1600/image.jpeg " height= " 124 " width= " 320 " / > < /a > When the < a href= " http://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.4/ " target= " _blank " > Zv9 < /a > assembly was released in July 2010, the zebrafish genome sequence was given into ...
Source: GenomeRef - September 17, 2014 Category: Genetics & Stem Cells Source Type: blogs
