OMIA is being migrated again!:
To overcome a chronic problem encountered with the previous migration, OMIA has to be migrated again. Unfortunately, this means that OMIA will be unavailable for 16 hours this week. I apologise for the inconvenience this will cause. The dates and times of the outage are:
Sydney: from Tues 20 Oct 5.00 pm until Wed 21 Oct 9:00 am (AEDT; UTC/GMT + 11 hours)
Some other locations:
Auckland: from Tues 20 Oct 2020 at 7:00 pm until Wed 21 Oct at 11:00 am
Tokyo: from Tues 20 Oct 2020 at 3:00 pm until Wed 21 Oct at 7:00 am
Beijing: from Tues 20 Oct 2020 at 2:00 pm until Wed 21 Oct at 6:00 am
New Delhi: from Tues 20 Oct 2020 at 11:30 am until Wed 21 Oct at 3:30 am
Moscow: from Tues 20 Oct 2020 at 9:00 am until Wed 21 Oct at 1:00 am
Paris: from Tues 20 Oct 2020 at 8:00 am until Wed 21 Oct at 12:00 midnight
London: from Tues 20 Oct 2020 at 7:00 am until Tues 20 Oct at 11:00 pm
Buenos Aires: from Tues 20 Oct 2020 at 3:00 am until Tues 20 Oct at 7:00 pm
New York: from Tues 20 Oct 2020 at 2:00 am until Tues 20 Oct at 6:00 pm
Los Angeles: Mon 19 Oct 2020 at 11:00 pm until Tues 20 Oct at 3:00 pm
Another possible OMIA outage:
Not surprisingly, a couple of issues have emerged with OMIA after the recent migration. Some users may have noticed that there were brief outages last weekend. Attempts to resolve these issues may result in outages over the next few days, i.e. from 1 October. I will post another notice as soon as everything is back to normal.
OMIA migration successful?:
The migration of OMIA to a new server seems to have been successful. Please let me know if you encounter any probelms.
HAPPY 25th BIRTHDAY, OMIA!:
On 26th May 1995, OMIA was launched on a server hosted at the University of Sydney. The 25th anniversary virtual celebration is announced in a webpage that provides links to three videos. Sincere thanks are due to the many people who have enabled OMIA to function and grow over these 25 years. They are named and thanked under the OMIA Acknowledgements tab. Their invaluable contributions are much appreciated.
HAPPY MENDEL DAY 2020!:
Yesterday (8th March; I missed it by a day!) marks the 155th anniversary of Mendel completing the reading of his paper to the Natural History Society of Brünn (Brno in the Czech Republic) in 1865. Mendel Day sits symbolically between Darwin Day in February and DNA Day in April, neatly replicating the chronology of three of the most important discoveries in biology.
OMIA is fundraising:
From 18 March 2019, users will see a fundraising popup once a month when they access this website. The popup is also viewable anytime from the Donate tab on the home page. OMIA's venture into this form of fundraising follows that of OMIM (on which OMIA is modelled) which has been conducting a popup-fundraising scheme since 2016. It is hoped to raise sufficient funds to retain a part-time software engineer for maintenance and enhancements, and (in the longer term) to retain a part-time head curator when Frank Nicholas is no longer able to fulfil that role.
ANOTHER OMIA UPGRADE!:
Yet another major upgrade of OMIA was launched on 14th November 2018. The new version reflects a comprehensive upgrade of the computing infrastructure, including establishment of a secure https protocol. It also includes a text-mining tool for curators that will greatly enhance the efficiency of curation. The tool starts with daily PubTator annotations of PubMed abstracts, and then feeds selected abstracts into a pipeline that includes a taxonomy filter and screening by a machine-learning classifier. The result is around 5 PubMed IDs being deposited into the OMIA publication curation tool each day, from the approximately 5000 new abstracts added to PubMed each day. The upgrade also includes a few specific enhancements, such as presenting the results of all searches in tabular form. Due to illness of the software engineer who developed these specific enhancements, some of them (including the tables) are not yet fully functional.
HAPPY MENDEL DAY!:
Today (8th March 2018) marks the 153rd anniversary of Mendel completing the reading of his paper to the Natural History Society of Brünn (Brno in the Czech Republic). Mendel Day sits symbolically between Darwin Day in February and DNA Day in April, neatly replicating the chronology of three of the most important discoveries in biology.
A NEW VERSION OF OMIA!:
OMIA has two new features: 1. a new URL (http://omia.org) (the old one redirects to the new one)
2. sortable tables of likely causal variants in (more-or-less) standard format. For more details, see the user guide available from the Help tab.
MENDEL DAY: 8th March 2017:
Professor Eva Matalova and her colleagues in the Mendelianum in Brno have arranged a wonderful program for Mendel Day 2017, including a guided walking Mendel tour of Brno; an exhibition; a concert of violin music of Leos Janacek, who, as a former organ scholar in Mendel's monastery, arranged the music and played the organ at Mendel's requiem mass; and (on 9th March) a trip to Vienna for a tour of sites associated with Mendel's student days. For details see the Mendelianum website.
First large-scale screening of disease-implicated variants across purebred dogs:
By genotyping of 6,788 dogs from 233 breeds for 93 disease-implicated variants across 80 single-locus disorders, Donner et al. (2016) have provided a very informative "snapshot" of the distribution and frequency of these variants across breeds. Among other things, the results indicate that certain disease-implicated variants occur in more breeds than was previously thought.
Reverse genomics reveals genetic load:
In a landmark project, Michot et al. (2016) analysed the genomic sequence of 1147 bulls (representing 15 European breeds) from the 1000 bull genome project, yielding "2489 putative deleterious variants (stop lost and gained, frameshift, splice acceptor and donor sites, initiator codon variants and missense variants predicted as deleterious with a score of 0 by SIFT) that segregated at a frequency of 5 % or more in at least one of the 15 breeds represented by at least 20 genomes in run 4 of the 1000 bull genomes project". As a proof-of-principle illustration of the nature of these variants, Michot et al. (2016) "investigated the phenotypic consequences of a frameshift variant in the retinitis pigmentosa-1 gene segregating in several breeds and at a high frequency (27 %) in Normande cattle . . . [that] causes progressive degeneration of photoreceptors leading to complete blindness in homozygotes". See OMIA 002029/9913
The genetic basis of evolution in Galapagos finches:
In some ground-breaking research showing the enormous potential of whole-genome sequence data in "unmapped" species, Leif Andersson has teamed with Peter and Rosemary Grant and other colleagues to identify two genes that have played a major role in the evolution of beak shape and beak size in the so-called Darwin finches of the Galapagos Islands. See OMIA 001945-48881 and OMIA 001992-48881.
HAPPY MENDEL DAY!:
Today (8th March) marks the 151st anniversary of Mendel completing the reading of his paper to the Brno Nature Science Society; a paper that, without Mendel ever realising it, paved the way for our ever-increasing understanding of life on earth. On this day we should also remember the English biologist William Bateson, who, in 1900, was the first person to fully comprehend the universality of Mendel's hypothesis, and who, as described in the Landmarks tab of this website, rapidly demonstrated this universality in animals.
Mendel Day: 8th March:
To mark the 150th anniversary of the publication of Mendel's paper in the journal of the Nature Science Society in Brno, Professor Eva Matalova and her colleagues in the Mendelianum in Brno have proposed that 8th March be celebrated as Mendel Day. The March timing of Mendel Day symbolically fits between Darwin Day in February and DNA Day in April, neatly replicating the chronology of three of the most important discoveries in biology. Geneticists around the world are encouraged to mark this event. Details are available from the Mendelianum website.
An ancient 'supergene' with profound effects on male breeding behaviour, body size and plumage colour:
The ruff is a Eurasian shorebird that has a spectacular lekking behaviour where highly ornamented males compete for females. On 16 November 2015, two groups have simultaneously reported that males with alternative reproductive strategies carry a chromosomal rearrangement that has been maintained as a balanced genetic polymorphism for about 4 million years. (text based on a press release from Uppsala University)
HAPPY 20th BIRTHDAY OMIA!:
On 26th May 1995, the online version of Mendelian Inheritance in Animals first went public, signalling the birth of OMIA. Details of the history of OMIA, and of its predecessor MIA, including mention of many people who have been involved over the years, are available under the Acknowledgements tab just above this notice.
Exactly 150 years ago, on 8 February and 8 March 1865, Johann (Gregor) Mendel read his paradigm-shifting paper Versuche über Pflanzenhybriden (Experiments on Plant Hybridization) to the Natural History Society of Brünn (Brno in the Czech Republic), reporting the results of eight years of experimental crosses among different (inbred) varieties of the garden pea, Pisum sativum. The paper was published the following year in the proceedings of the Society (Verhandlungen des naturforschenden Vereins Brünn). The original paper (in German) and an English translation (based on C. T. Druery's original translation done for William Bateson) are both available online: German; English.
Third and final chicken comb gene resolved:
19 March 2015: Dorshorst et al. (2015) have reported the molecular basis of the third of the three classic comb types in chickens. This third type (Duplex) turns out to be due to a large (20kb) "duplication . . . located 200 Kb upstream of EOMES, a gene that was found to be abnormally expressed in the comb-developing region of Vshaped and Buttercup comb chicken embryos". As the authors also report, "These findings complete our characterization of the genetic basis of the three major comb loci in the chicken, all of which are caused by large-scale structural genomic variants that drive ectopic expression of transcription factors in the comb region during chicken embryo development".
Haplotype tests for recessive disorders that affect fertility and other traits:
31 October 2014: USDA researchers J.B. Cole, P.M. VanRaden, D.J. Null, J.L. Hutchison, T.A. Cooper, and S.M. Hubbard have summarised the latest information about haplotypes affecting fertility and other traits in cattle on their Animal Improvement Program website. Their table contains hyperlinks to relevant OMIA entries.
OMIA mirror at NCBI decommissioned:
16th April 2014: NCBI has decommissioned its OMIA mirror, due to funding constraints. All OMIA traffic to NCBI is now redirected to this home site. All OMIA links to NCBI remain functional from this home site. Discussions are underway for the establishment of links to OMIA from various relevant NCBI resources.
Review of OMIA causal/key variants:
26 December 2013: An open-access review of the discovery of causal/key variants in non-laboratory animals has been published in Animal Genetics.
Balancing selection at the polled/horns locus:
21 August 2013: A fascinating evolutionary story concerning the polled/horns locus in Soay sheep has been uncovered by Johnston et al. (2013). This has all the hallmarks of a classic textbook example of heterozygote advantage (overdominance) for fitness.
Manx taillessness resolved:
15 August 2013: Buckingham et al. (2013) have reported mutations in the T gene that are causal for the various short-tail phenotypes characteristic of Manx cats. Short tail in Manx cats was the first feline trait to be documented as Mendelian (by Bateson in his 1909 book "Mendel’s Principles of Heredity"). Mutations in the homologous genes in dogs and mice give rise to similar phenotypes.
DNA tests for canine and feline hereditary diseases:
In February 2013, a new web site was launched to provide up-to-date information on the availability of DNA tests for canine and feline single-locus disorders. For background, see Slutsky et al. (2013) Veterinary Journal
Key locomotion mutation identified:
On 29 August, in a paper in Nature, Andersson et al. (2012) reported a nonsense mutation in DMRT3, which encodes a transcription factor, that plays a major role in determining mode of locomotion. For more information, and access to a copy of the paper, see Gaitedness.
Two iconic Mendelian traits resolved in a week! :
One hundred and ten years after they were first described as Mendelian (single-locus) traits, the last two of the six originally-described Mendelian traits have been resolved (or partly so) at the molecular level within a week of each other! On 21 June 2012, Medugorac et al. (PLoS ONE 7(6): e39477) described two bovine alleles (both complex indels) that are completely associated with Polledness in cattle of European origin. One week later (28 June 2012), Imsland et al. (PLoS Genet 8(6): e1002775) reported two chicken alleles (a very large (7.38Mb) inversion and another complex rearrangement derived from that inversion) that give rise to the Rose-comb phenotype in chickens. The chicken inversion results in "the relocalization of the MNR2 homeodomain protein gene leading to transient ectopic expression of MNR2 during comb development". Mysteriously, neither of the bovine polled alleles disrupts "any known coding sequence or a splice site, or an intronic region, or any known regulatory regions". Posted 30 June 2012
Vale Alan Wilton:
Among many other things, Alan Wilton was a very active and highly-regarded member of the global research community devoted to identifying the causal mutations for inherited diseases in dogs. He died on 14th October 2011, aged 58, still in his intellectual prime. His publications in canine inherited diseases were concerned with Cerebellar abiotrophy, Neuronal ceroid lipofuscinosis 5, Neuronal ceroid lipofuscinosis 8, and Trapped Neutrophil Syndrome. For the second and fourth of these disorders, he was instrumental in discovering the causal mutation. As a colleague and friend, he is sorely missed.UNSW tribute
Two new books:
Introduction to Veterinary Genetics
(3rd edn; 2010) by Frank Nicholas
Breed Predispositions to Disease in Dogs and Cats
(2nd edn; 2010) by Alex Gough and Alison Thomas
New website launched:
This new OMIA website was launched on 10 August 2011. It has a cleaner look and improved tools for data curators. It is powered by django and is simpler and more efficient "under the hood".
Vale Victor A. McKusick, MD:
The creator of Mendelian Inheritance in Man and its online version OMIM, Dr Victor McKusick, died on July 22nd, 2008. As mentioned in the Acknowledgements, Dr McKusick was instrumental in providing encouragement for the creation of OMIA from 1978 onwards, and in enabling OMIA to be made publicly available in 1995. He continued to provide strong moral support for OMIA until his death. For obituaries, see ASHG and Johns Hopkins Medicine. For extensive information on the life and career of Dr McKusick, visit the McKusick archives.