198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/makeDb/trackDb/human/hg18/cnp.html src/hg/makeDb/trackDb/human/hg18/cnp.html index b75f4614a38..1f6a2657ac1 100644 --- src/hg/makeDb/trackDb/human/hg18/cnp.html +++ src/hg/makeDb/trackDb/human/hg18/cnp.html @@ -1,332 +1,332 @@ <H2>Description</H2> <P> This annotation shows regions detected as putative copy number polymorphisms (CNP) and sites of detected intermediate-sized structural variation (ISV). The CNPs and ISVs were determined by various methods, displayed in individual subtracks within the annotation:</P> <UL> <LI> <B>Deletions from genotype analysis (Conrad):</B> 935 deletions detected by analysis of SNP genotypes, using the HapMap Phase I data, release 16c.1, CEU and YRI samples. <LI> <B>Deletions from haploid hybridization analysis (Hinds):</B> 100 deletions from haploid hybridization analysis in 24 unrelated individuals from the Polymorphism Discovery Resource, selected for SNP LD study. <LI> <B>BAC microarray analysis (Iafrate):</B> 236 putative CNP regions detected by BAC microarray analysis in a population of 55 individuals, 16 of which had previously-characterized chromosomal abnormalities. The group consisted of 10 Caucasians, 4 Amerindians, 2 Chinese, 2 Indo-Pakistani, 2 Sub-Saharan African, and 35 of unknown ethnic origin. <LI> <B>CNP in duplication-rich regions (Locke):</B> 243 CNP regions were identified using array CGH in the HapMap populations (269 individuals). The study was specific to 130 putative rearrangement hotspot regions. <LI> <B>Deletions from genotype analysis (McCarroll):</B> 540 deletions detected by analysis of SNP genotypes, using the HapMap Phase I data, release 16a. <LI> <B>SNP and BAC microarray analysis of HapMap data (Redon):</B> 1,445 copy number variable regions found in the HapMap Phase II data. <LI> <B>Representational oligonucleotide microarray analysis (ROMA) (Sebat):</B> 80 putative CNP regions detected by ROMA in a population of 20 normal individuals comprised of 1 Biaka, 1 Mbuti, 1 Druze, 1 Melanesian, 4 French, 1 Venezualan, 1 Cambodian, 1 Mayan and 9 of unknown ethnicity. <LI> <B>BAC microarray analysis (Sharp):</B> 140 putative CNP regions detected by BAC microarray analysis in a population of 47 individuals comprised of 8 Chinese, 4 Japanese, 10 Czech, 2 Druze, 7 Biaka, 9 Mbuti, and 7 Amerindians. <LI> <B>Fosmid mapping (Tuzun):</B> 297 ISV sites detected by mapping paired-end sequences from a human fosmid DNA library. </UL></P> <H2>Display Conventions and Configuration</H2> <P> CNP and ISV regions are indicated by solid blocks that are color-coded to indicate the type of variation detected: <UL> <LI> <B><FONT COLOR="green">Green</FONT>:</B> gain (duplications) <LI> <B><FONT COLOR="red">Red</FONT>:</B> loss (deletions) <LI> <B><FONT COLOR="blue">Blue</FONT>:</B> gain and loss (both deletion and duplication) <LI> <B>Black:</B> inversion <LI> <B><FONT COLOR="gray">Gray</FONT>:</B> gain or loss (unknown direction) </UL></P> <P>Note that display IDs are not preserved between assemblies.</P> <H3>Conrad subtrack</H3> <P> The method used to identify these deletions approximates the breakpoints of each event; therefore, a set of minimal and maximal endpoints is associated with each deletion. Thick lines delineate the minimally deleted region; thin lines delineate the maximally deleted region. <H3>Sharp subtrack </H3> <P> On the details pages for elements in this subtrack, the table shows value/threshold data for each individual in the population. "Value" is defined as the log<sub>2</sub> ratio of fluorescence intensity of test versus reference DNA. "Threshold" is defined as 2 standard deviations from the mean log<sub>2</sub> ratio of all autosomal clones per hybridization. The "Disease Percent" value reflects the percent of the BAC that lies within a "rearrangement hotspot", as defined in Sharp <em>et al</em>. (2005). A rearrangement hotspot is defined by the presence of flanking intrachromosomal duplications >10 kb in length with >95% similarity and separated by 50 kb - 10 Mb of intervening sequence.</P> <H2>Methods</H2> <H3>Conrad genotype analysis</H3> <P> SNPs in regions that are hemizygous for a deletion are generally miscalled as homozygous for the allele that is present. Hence, when a deletion is transmitted from parent to child, the genotypes at SNPs within the deletion region will often appear to violate the rules of Mendelian transmission. The authors developed a simple algorithm for scanning trio data for unusual runs of consecutive SNPs that, in a single family, have genotype configurations consistent with the presence of a deletion. <H3>Hinds haploid hybridization analysis</H3> <P> Approximately 600 Mb of genomic DNA from 24 unrelated individuals were obtained from the Polymorphism Discovery Resource. Haploid hybridization was used to identify genomic intervals showing a reduced hybridization signal in comparison to the reference assembly. PCR amplification was performed on 215 candidate deletions. 100 deletions were selected that were unambiguously confirmed. <H3>Iafrate BAC microarray analysis</H3> <P> All hybridizations were performed in duplicate incorporating a dye-reversal using proprietary 1 Mb GenomeChip V1.2 Human BAC Arrays consisting of 2,632 BAC clones (Spectral Genomics, Houston, TX). The false positive rate was estimated at ~1 clone per 5,264 tested. </P> <P> Further information is available from the <A HREF="http://projects.tcag.ca/variation/" TARGET=_blank>Database of Genomic Variants</A> website.</P> <H3>Locke analysis of duplication-rich regions</H3> <P> DNA samples were obtained from Coriell Cell Repositories. The reference DNA used for all hybridizations was from a single male of Czechoslovakian descent, Coriell ID GM15724 (also used in the Sharp study). <P> A locus was considered a CNV (copy number variation) if the log ratio of fluroescence measurements for the individuals assayed exceeded twice the standard deviation of the autosomal clones in replicate dye-swapped experiments. A CNV was classified as a CNP if altered copy number was observed in more than 1% of the 269 individuals. <H3>McCarroll genotype analysis</H3> <P> A segregating deletion can leave "footprints" in SNP genotype data, including apparent deviations from Mendelian inheritance, apparent deviations from Hardy-Weinberg equilibrium and null genotypes. Using these clues to discover true variants is challenging, however, because the vast majority of such observations represent technical artifacts and genotyping errors. </P> <P> To determine whether a subset of "failed" SNP genotyping assays in the HapMap data might reflect structural variation, the authors examined whether such failures were physically clustered in a manner that is specific to individuals. Consistent with this hypothesis, the rate of Mendelian-inconsistent genotypes was elevated near other Mendelian-inconsistent genotypes in the same individual but was unrelated to Mendelian inconsistencies in other individuals. </P> <P> The authors systematically looked for regions of the genome in which the same failure profile appeared repeatedly at nearby markers in a manner that was statistically unexpected based on chance. A set of statistical thresholds was tailored to each mode of failure, genotyping center and genotyping platform used in the project. The same procedure could readily apply to dense SNP data from any platform or study.</P> <H3>Redon analysis of HapMap data</H3> <P>Experiments were performed with the International HapMap DNA and cell-line collection using two technologies: comparative analysis of hybridization intensities on Affymetric GeneChip Human Mapping 500K early access arrays (500K EA) and comparative genomic hybridization with a Whole Genome TilePath (WGTP) array. <H3>Sebat ROMA</H3> <P> Following digestion with BglII or HindIII, genomic DNA was hybridized to a custom array consisting of 85,000 oligonucleotide probes. The probes were selected to be free of common repeats and have unique homology within the human genome. The average resolution of the array was ~35 kb; however, only intervals in which three consecutive probes showed concordant signals were scored as CNPs. All hybridizations were performed in duplicate incorporating a dye-reversal, with the false positive rate estimated to be ~6%.</P> <H3>Sharp BAC microarray analysis</H3> <P> All hybridizations were performed in duplicate incorporating a dye-reversal using a custom array consisting of 2,194 end-sequence or FISH-confirmed BACs, targeted to regions of the genome flanked by segmental duplications. The false positive rate was estimated at ~3 clones per 4,000 tested.</P> <H3>Tuzun fosmid mapping</H3> <P> Paired-end sequences from a human fosmid DNA library were mapped to the assembly. The average resolution of this technique was ~8 kb, and included 56 sites of inversion not detectable by the array-based approaches. However, because of the physical constraints of fosmid insert size, this technique was unable to detect insertions greater than 40 kb in size.</P> <H2>Validation</H2> <H3>Conrad genotype analysis</H3> <P> The authors first tested 12 predicted deletions using quantitative PCR. For all 12 deletions, DNA concentrations consistent with transmission of a deletion from parent to child were observed.</P> <P>To provide more extensive validation by comparative genome hybridization (CGH), the authors designed a custom oligonucleotide microarray comprised of 380,000 probes that tile across all 134 candidate deletions identified in 9 HapMap offspring (8 YRI and 1 CEU). The results of this CGH analysis indicate that the majority (about 85%) of candidate deletions detected by the method are real. <H3>Locke duplication-rich regions </H3> The authors performed validation using a custom oligonucleotide array, hybridized to 9 of the HapMap individuals. Their analysis of the validation experiments indicated a false-negative rate of 5% and a false-positive rate of less than 0.2%. <H3>McCarroll genotype analysis</H3> <P> Four methods of validation were used: fluorescent <em>in situ</em> hybridization (FISH), two-color fluorescence intensity measurements, PCR amplification and quantitative PCR. </P> <P> The authors performed fluorescent <em>in situ</em> hybridization for five candidate deletions large enough to span available FISH probes. In all five cases, FISH assays confirmed the deletions in the predicted individuals. </P> <P> The authors examined two-color allele-specific fluorescence data from SNP genotyping assays from a data subset available at the Broad Institute, looking for a reduction in fluorescence intensity in individuals predicted to carry a deletion. At most SNPs in the genome, fluorescence intensity measurements clustered into two or three discrete groups corresponding to homozygous and hetrozygous genotypes. At 15 of 17 candidate deletion loci, fluorescence intensity data for one or more SNPs clustered into additional groups that corresponded to the predicted deletion genotypes. </P> <P> The authors used PCR amplification to query 60 loci for which the pattern of genotypes suggested multiple individuals with homozygous deletions. Variants were considered confirmed if the pattern of amplification success and failure matched prediction across a set of 12-24 individuals. The authors confirmed 51 of 60 candidate variants by this criterion. </P> <P> The authors performed quantitative PCR in all 269 HapMap DNA samples for 11 candidate deletions that overlapped the coding exons of genes and that were discovered in many individuals. At 10/11 loci, the authors observed three discrete clusters, identifying individuals with zero, one and two gene copies. All 60 trios displayed Mendelian inheritance for the ten deletions, as well as Hardy-Weinberg equilibrium in all four populations surveyed, and transmission rates close to 50%. This suggests that the deletions behave as a stable, heritable genetic polymorphism. </P> <H3>Redon analysis of HapMap data</H3> -The authors utilized numerous quality meaures, including repeated experiments +The authors utilized numerous quality measures, including repeated experiments on the WGTP array for 82 individuals and on the 500K EA array for 15 individuals. The average false-positive rate per experiment was held beneath 5%. Aberrant chromosomes were removed from the analysis. </P> <H2>Credits</H2> <P> Thanks to Lars Feuk at <A HREF="https://www.sickkids.ca/" TARGET=_blank>The Hospital for Sick Children in Toronto</A> for providing these data in hg18 coordinates. </P> <H2>References</H2> <P> Feuk L, Carson AR, Scherer SW. <A HREF="https://www.nature.com/articles/nrg1767" TARGET=_blank> Structural variation in the human genome</A>. <em>Nat Rev Genet</em>. 2006 Feb;7(2):85-97. </P> <P> Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. <A HREF="https://www.nature.com/articles/ng1697" TARGET=_blank>A high-resolution survey of deletion polymorphism in the human genome</A>. <em>Nat Genet.</em> 2006 Jan;38(1):75-81. </P> <P> Hinds DA, Kloek AP, Jen M, Chen X, Frazer KA. <A HREF="https://www.nature.com/articles/ng1695" TARGET=_blank>Common deletions and SNPs are in linkage disequilibrium in the human genome</A>. <em>Nat Genet.</em> 2006 Jan;38(1):82-5. </P> <P> Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. <A HREF="https://www.nature.com/articles/ng1416" TARGET=_blank>Detection of large-scale variation in the human genome</A>. <em>Nat Genet.</em> 2004 Sep;36(9):949-51.</P> <P> Locke DP, Sharp AJ, McCarroll SA, McGrath SD, Newman TL, Cheng Z, Schwartz S, Albertson DG, Pinkel D, Altshuler DM <em>et al</em>. <A HREF="https://www.ajhg.org/AJHG/abstract/S0002-9297(07)63135-8" TARGET=_blank> Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome</A>. <em>Am J Hum Genet.</em> 2006 Aug;79(2):275-90.</P> <P> McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, Dallaire S, Gabriel SB, Lee C, Daly MJ <em>et al</em>. <A HREF="https://www.nature.com/articles/ng1696" TARGET=_blank>Common deletion polymorphisms in the human genome</A>. <em>Nat Genet.</em> 2006 Jan;38(1):86-92.</P> <P> Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W <em>et al</em>. <A HREF="https://www.nature.com/articles/nature05329" TARGET=_blank> Global variation in copy number in the human genome</A>. <em>Nature.</em> 2006 Nov 23;444(7118):444-454. <P> Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M <em>et al</em>. <A HREF="https://science.sciencemag.org/content/305/5683/525" TARGET=_blank>Large-scale copy number polymorphism in the human genome</A>. <em>Science.</em> 2004 July 23;305(5683):525-8.</P> <P> Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R <em>et al</em>. <A HREF="https://www.cell.com/ajhg/abstract/S0002-9297(07)63135-8" TARGET=_blank>Segmental duplications and copy number variation in the human genome</A>. <em>Am J Hum Genet.</em> 2005 Jul;77(1):78-88.</P> <P> Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K <em>et al</em>. <A HREF="https://www.nature.com/articles/ng754" TARGET=_blank>Assembly of microarrays for genome-wide measurement of DNA copy number</A>. <em>Nat Genet.</em> 2001 Nov;29(3):263-4.</P> <P> Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D <em>et al</em>. <A HREF="https://www.nature.com/articles/ng1562" TARGET=_blank>Fine-scale structural variation of the human genome</A>. <em>Nat Genet.</em> 2005 Jul;37(7):727-32.</P> Nguyen DQ, Webber C, Ponting CP. <A HREF="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020020" TARGET=_blank>Bias of selection on human copy-number variants</A>. <em>PLoS Genet</em>. 2006 Feb;2(2):e20.</P>