In cases where two copies of the same chromosome, or part of a chromosome, from one parent and no copies from the other parent are present in the cell, we call it uniparental disomy (UPD). While all DNA information is present, the development of the cell (and the organism) is hindered because of missing / wrong epigenetic markers. The basic mechanism of how this faulty distribution of chromosomes can occur, is shown in fig.1.
- Eggermann and Kotzot (2010) Uniparental disomy, Onset mechanisms and their relevance in clinical genetics [German], Medizinische Genetik
Besides the visual client, the version control system Perforce can be operated through the command line (unix prompt or windows Dos window) and therefor be controlled through other programs like MatLab:
[status, result] = dos(p4command);
A reference manual is available, here are a few hints:
Check the environment settings:
p4 set P4CHARSET=winansi P4CLIENT=try1 (set) P4EDITOR=C:\Windows\SysWOW64\notepad.exe (set) P4PORT=perforce:1666 P4USER=Felix_Kokocinski
end edit if necessary with
P4EDITOR is optional, P4CLIENT is the checkout / workspace name.
The settings can also be set permanently in the visual client under
Edit / Preferences / Connection / Change Settings
If these are wrong you will get messages like "file(s) not on client".
Most common commands:
p4 edit filename.txt or p4 edit //depot/path/in/perforce/filename.txt
p4 submit -d "description of changes" filename.txt
revert to version in repository:
p4 revert filename.txt
add new file:
p4 add filename.txt
Here are some useful one-liners for various tasks.
The Online Mendelian Inheritance in Man is a manually reviewed catalog of human genes and regions involved in genetic disorders and traits. Each entry has a name and a number, e.g. "#154780 MARSHALL SYNDROME". According to the OMIM FAQs, these are the meanings of the the symbols preceding a MIM number:
- An asterisk (*) before an entry number indicates a gene.
- A number symbol (#) before an entry number indicates that it is a descriptive entry, usually of a phenotype, and does not represent a unique locus. The reason for the use of the number symbol is given in the first paragraph of the entry. Discussion of any gene(s) related to the phenotype resides in another entry(ies) as described in the first paragraph.
- A plus sign (+) before an entry number indicates that the entry contains the description of a gene of known sequence and a phenotype.
- A percent sign (%) before an entry number indicates that the entry describes a confirmed mendelian phenotype or phenotypic locus for which the underlying molecular basis is not known.
- No symbol before an entry number generally indicates a description of a phenotype for which the mendelian basis, although suspected, has not been clearly established or that the separateness of this phenotype from that in another entry is unclear.
- A caret (^) before an entry number means the entry no longer exists because it was removed from the database or moved to another entry as indicated.
To fetch a non-redundant list of OMIM annotation through the Ensembl Perl API you can look at the external references (xrefs/dblinks):
The symbols to describe the different nucleotides in DNA are the following:
------------------------------------------ Symbol Meaning Nucleic Acid ------------------------------------------ A A Adenine C C Cytosine G G Guanine T T Thymine U U Uracil M A or C R A or G W A or T S C or G Y C or T K G or T V A or C or G H A or C or T D A or G or T B C or G or T X G or A or T or C N G or A or T or C
Note: these letters are also used in the "samtools tview" program to visually show NGS read alignments.
- IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE: Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030.
The goal of the 1000 Genomes Project is create a "A Deep Catalog of Human Genetic Variation" by measuring and analysing most genetic variants that have frequencies of at least 1% in the populations studied.
CHB Han Chines Han Chinese in Beijing, China JPT Japanese Japanese in Tokyo, Japan CHS Southern Han Chinese Han Chinese South CDX Dai Chinese Chinese Dai in Xishuangbanna, China KHV Kinh Vietnamese Kinh in Ho Chi Minh City, Vietnam CHD Denver Chinese Chinese in Denver, Colorado (pilot 3 only) CEU CEPH Utah residents (CEPH) with Northern and Western European ancestry TSI Tuscan Toscani in Italia GBR British British in England and Scotland FIN Finnish Finnish in Finland IBS Spanish Iberian populations in Spain YRI Yoruba Yoruba in Ibadan, Nigeria LWK Luhya Luhya in Webuye, Kenya GWD Gambian Gambian in Western Division, The Gambia MSL Mende Mende in Sierra Leone ESN Esan Esan in Nigeria ASW African-American SW African Ancestry in Southwest US ACB African-Caribbean African Caribbean in Barbados MXL Mexican-American Mexican Ancestry in Los Angeles, California PUR Puerto Rican Puerto Rican in Puerto Rico CLM Colombian Colombian in Medellin, Colombia PEL Peruvian Peruvian in Lima, Peru GIH Gujarati Gujarati Indian in Houston,TX PJL Punjabi Punjabi in Lahore,Pakistan BEB Bengali Belgali in Bangladesh STU Sri Lankan Sri Lankan Tamil in the UK ITU Indian Indian Telugu in the UK