Frequently Asked Questions
- When are you going to update the assembly next?
- How do I use alternate loci and patches?
- What MHC haplotypes are used in the assembly?
- What LRC haplotypes are used in the assembly?
- When are you going to update the assembly next?
- Currently, we don't have a set schedule for major genome updates (major updates involve disrupting chromosome coordinates). When we start to plan for a major assembly update, we will make an announcement via the GRC news. As we get more defined timelines, we will continue to update the community via the news feed. Once the GRC has released a major update for an assembly, patch updates will occur quarterly if there is sufficient data to release a patch.
- How do I use alternate loci and patches?
- Alternate loci are meant to represent allelic diversity. When possible, we put the altenate locus into chromosome context via alignments. Both the alignments and a file showing the region of the chromosome to which the alternate aligns are released with the assembly. Patches are released in the same way as the alternate loci.
- What MHC haplotypes are used in the assembly?
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We use sequences defined by the MHC consortium.
MHC Haplotype Data GenBank ID RefSeq ID Assembly Unit Clone Library Cell Line Haplotype CM000668.1 NC_000006.11 Primary CH501 PGF A3-B7-DR15 GL000250.1 NT_167244.1 alt ref loci 1 DAAP APD A1-B60-DR13 GL000251.1 NT_113891.2 alt ref loci 2 CH502 COX A1-B8-DR3 GL000252.1 NT_167245.1 alt ref loci 3 DADB DBB A2-B57-DR7 GL000253.1 NT_167246.1 alt ref loci 4 DAMA MANN A29-B44-DR7 GL000254.1 NT_167247.1 alt ref loci 5 DAMC MCF A2-B62-DR4 GL000255.1 NT_167248.1 alt ref loci 6 DAQB QBL A26-B18-DR3 GL000256.1 NT_167349.1 alt ref loci 7 DASS SSTO A32-B44-DR4 - What LRC Haplotypes are used in the reference assembly?
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LRC haplotypes are described in the following publications: Traherne et al., 2010, Horton et al., 2006, and Barrow and Trowsdale, 2008.
More information can be found LRC Haplotype Project Page
LRC Haplotype Information GenBank ID RefSeq ID Assembly Unit Clone Library Haplotype CM000681.1 NT_000019.9 Primary mixed mixed GL949746.1 NW_003571054.1 patches CH502 COX1 GL949747.1 NW_003571055.1 patches CH502 COX2 GL949748.1 NW_003571056.1 patches XX-FLRC LRC_i GL949749.1 NW_003571057.1 patches XX-FLRC LRC_j GL949750.1 NW_003571058.1 patches XX-FLRC LRC_s GL949751.1 NW_003571059.1 patches XX-FLRC LRC_t GL949752.1 NW_003571060.1 patches CH501 PGF1 GL949753.1 NW_003571061.1 patches CH501 PGF2