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======Oncoarray Consortium Wiki: Dartmouth Edition======

These pages are for sharing information among the consortia genotyping the Illumina Oncoarray chip.

There are various [[Oncoarray:analysis_groups|groups involved in this analysis]]

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===== Genotype Calling =====

Information regarding genotype calling at Dartmouth can be found {{:genotype_calling.docx|here.}}

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===== Positions/Strands =====
This {{:onco_positions_strands.zip|list}} has the strands the TOP alleles from the Oncoarray chip refer to. Most strands were determined by blasting the probe sequence against 1KG sequencing. Some unknown strands were changed to reflect the alleles of the 1KG variant matched to the SNP. Some ambiguous SNPs were flipped to match the expected frequency of the 1KG. Some positions for SNPs with rs numbers were updated to match dbSNP and the probe sequence was confirmed to be in the amended position. The positions for Indels matched to 1KG variants have been amended to match the 1KG system of numbering (i.e. one less than the manifest position.)

The SNPs that have been matched to 1KG variants and their alleles are listed in this {{:onco_all_pos_1kg_alleles.zip|file.}}

Descriptions of retrieving your requesting markers in OncoArray data can be found {{:descriptions_of_retrieving_your_requesting_markers_in_oncoarray_data.pdf|here.}}

The List of Probe Sequences can be found in this file 
{{ :oncoarray_probe_sequencing_.xlsx | here }}
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===== Quality Control Components =====

==== QC Process ====
The QC process is documented {{:oncoarray_qc_guidelines_v8_1.doc|here.}}

The number of SNPs excluded at each step is summarized in this {{:oncoarray_qc_guidelines_v8_1.doc|file.}}

=== SNP QC Exclusion Lists ===
== Duplicate Probes ==
There are a number of variants on the chip with the same probe in the same position (or a few with the same alleles but the sequence from the opposite strand.) The probe with the worse QC scores and call rate is chosen for exclusion.

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===== Tracking of Incoming Data =====

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===== Link To Proposals =====

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=== SNPs for Sex Checking ===
For checking the sex of samples use the 300 Y markers confirmed to work in males and to have a non-autosomal pattern in their cluster plots, seen in this [[http://consortia.ccge.medschl.cam.ac.uk/oncoarray/lib/exe/fetch.php?media=chr_y_snps_for_sex_checking.csv|list.]] In addition chromosome X SNPs that have many heterozygous calls in males and/or autosomal cluster plots should be not be used for sex checks.

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==== SNPs to Exclude before Imputation ====
The list used in Cambridge of 49,659 SNPs to exclude before producing imputation input files [[http://consortia.ccge.medschl.cam.ac.uk/oncoarray/lib/exe/fetch.php?media=onco_exclusions_from_imputation_input_v3.txt|is available.]]

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==== Completed Analyses ====

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==== Lung and Head and Neck Oncoarray project ====
{{:duplicates-report-reformattedgood.xlsx|Duplicate report}} for samples from the Lung and Head and Neck Oncoarray project.

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==== Other Pages Containing Information ====
  * [[Lung AffymetrixArray|Lung AffymetrixArray]]
  * [[TRICL]]

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