c3410576391423b865b4014a849c8dfc7c25bea0 hiram Tue Jun 9 13:42:14 2020 -0700 files for Codis hub and sessions refs #21399 diff --git src/hg/makeDb/doc/codisHub/codis.html src/hg/makeDb/doc/codisHub/codis.html new file mode 100644 index 0000000..c70501a --- /dev/null +++ src/hg/makeDb/doc/codisHub/codis.html @@ -0,0 +1,129 @@ +<h2>Description</h2> +<p> +This description is taken from: +<em>National Institute of Standards and Technology</em> +<a href="https://strbase.nist.gov/intro.htm" +target=_blank>Brief Introduction to STRs</a>. +</p> +<p> +Tandemly repeated DNA sequences are widespread throughout the human genome +and show sufficient variability among individuals in a population that they +have become important in several fields including genetic mapping, linkage +analysis, and human identity testing. These tandemly repeated regions of DNA +are typically classified into several groups depending on the size of the +repeat region. Minisatellites (variable number of tandem repeats, VNTRs) have +core repeats with 9-80 bp, while microsatellites (short tandem repeats, STRs) +contain 2-5 bp repeats. The forensic DNA community has moved primarily towards +tetranucleotide repeats, which may be amplified using the polymerase chain +reaction (PCR) with greater fidelity than dinucleotide repeats. The variety of +alleles present in a population is such that a high degree of discrimination +among individuals in the population may be obtained when multiple STR loci +are examined. +</p> +<p> +The region definitions are obtained from: +<em>National Institute of Standards and Technology</em> +<a href="https://strbase.nist.gov/fbicore.htm" +target="_blank">FBI CODIS Core STR Loci</a> +</p> + +<pre> + +gene genomic location repeating sequences (STRs) +locus + +TPOX chr2:1,489,568-1,489,738 AATG +D3S1358 chr3:45,540,612-45,540,935 TCTA/TCTG +FGA chr4:154,587,511-154,588,005 TTTC/TTTT/TTCT/CTTT/CTCC/TTCC +D5S818 chr5:123,775,262-123,775,937 AGAT +CSF1PO chr5:150,076,172-150,076,490 AGAT +D7S820 chr7:84,159,945-84,160,482 GATA +D8S1179 chr8:124,894,738-124,895,197 TCTA/TCTG +TH01 chr11:2,170,711-2,171,770 AATG/ATG +VWA chr12:5,983,825-5,984,174 TCTA/TCTG/TCCA +D13S317 chr13:82,147,846-82,148,218 TATC/AATC +D16S539 chr16:86,352,320-86,352,912 GATA +D18S51 chr18:63,281,248-63,282,317 AGAA +D21S11 chr21:19,181,866-19,182,275 TCTA/TCTG +AMELX chrX:11,296,605-11,296,939 polymorphism +AMELY chrY:6,869,982-6,870,187 polymorphism + +01 Jan 2017 added: +D1S1656 chr1:230,769,329-230,769,904 TAGA/TAGG +D2S441 chr2:68,011,777-68,012,172 TCTA +D2S1338 chr2:218,014,601-218,015,031 TGCC/TTCC +D10S1248 chr10:129,294,018-129,294,623 GGAA +D12S391 chr12:12,296,826-12,297,399 AGAT/AGAC +D19S433 chr19:29,925,974-29,926,466 AAGG/AAAG/TAGG +D22S1045 chr22:37,140,171-37,140,616 ATT/ACT +</pre> + +<h2>Display</h2> +<p> +All of these regions can be seen in one genome browser session using the +'multi-region' function to display them together as a set: +<a href="https://genome.ucsc.edu/s/Hiram/hg38.codis" +target=_blank">genome.ucsc.edu/s/Hiram/hg38.codis</a>. +</p> +<p> +The display indicates the regions of the genome amplified by the PCR primers, +the aligment of the PCR primers to the genome, and the repeating pattern of +the STR elements selected by the primers. +</p> + +<h2>Credits</h2> +<p> +This display was constructed by +<a HREF="mailto:hclawson@ucsc. +edu"> +Hiram Clawson</a> at the +<a href="https://ucscgenomics.soe.ucsc.edu" target="_blank">U.C. Santa Cruz Genomics Institute</a>. +</p> + +<h2>References</h2> + +<p> +National Institute of Standards and Technology +<a href="https://strbase.nist.gov/fbicore.htm" +target="_blank">FBI CODIS Core STR Loci</a> +</p> + +<p> +National Institute of Standards and Technology +<a href="https://strbase.nist.gov/str_fact.htm" +target="_blank">Overview of STR Fact Sheets</a> +with references to all publications for each of the STR systems. +</p> + +<p> +Erin Butler, Richard Li: CUNY John Jay College +<a href="https://academicworks.cuny.edu/jj_pubs/262/" +target="_blank">Genetic Markers for Sex Identification in Forensic DNA Analysis</a> 21 Aug 2014. +</p> + +<p> +Shadrach B, Commane M, Hren C, Warshawsky I. +<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1876427/" +target="_blank">A rare mutation in the primer binding region of the +amelogenin gene can interfere with gender identification.</a> +<em>J Mol Diagn.</em> 2004 Nov;6(4):401-5. doi: 10.1016/S1525-1578(10)60538-7. +PMID: 15507681; PMCID: PMC1876427. +</p> + +<p> +Grubwieser P, Mühlmann R, Parson W. +<a href="https://pubmed.ncbi.nlm.nih.gov/12799739/" +target="_blank">New Sensitive Amplification Primers for the STR Locus D2S1338 for Degraded Casework DNA</a> +<em>Int J Legal Med</em> 2003 Jun;117(3):185-8. doi: 10.1007/s00414-002-0359-y. +Epub 2003 Feb 11. +</p> + +<p> +Natsuko Mizuno, D.V.M.; Tetsushi Kitayama, M.Sc.; Koji Fujii, Ph.D.; +Hiroaki Nakahara, D.V.M.;Kanako Yoshida, Ph.D.; Kazumasa Sekiguchi, Ph.D.; +Naoto Yonezawa, Ph.D.; Minoru Nakano, Ph.D.; and Kentaro Kasai, Ph.D. +<a href="https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1556-4029.2008.00806.x" +target=_blank>A D19S433 Primer Binding Site Mutation and the Frequency in +Japanese of the Silent Allele It Causes</a> +<em>J. Forensic Sci,</em>September 2008, Vol. 53, No. 5 doi: 10.1111/j.1556-4029.2008.00806.x +</p>