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integrarray_qc_guidelines [2025/12/15 19:25] – Headings formatted 98.60.169.32integrarray_qc_guidelines [2025/12/23 16:14] (current) – [Molecular validation of findings.] 206.192.168.19
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 The figure below describes either i) classification of ancestry using PCA (shown by most likely descent ellipses) or ii) assignment of continental origin to individuals based on the closest location on the continental ancestry triangle. We prefer the latter approach as the ancestry can then be used as a covariate in analyses or for subsequent selection. The figure below describes either i) classification of ancestry using PCA (shown by most likely descent ellipses) or ii) assignment of continental origin to individuals based on the closest location on the continental ancestry triangle. We prefer the latter approach as the ancestry can then be used as a covariate in analyses or for subsequent selection.
 +{{ :cluster_in_pca_figure.png?500 |}}
  
 (All lists will become available on the Integarray wiki: https://www.integralu19.org/index.php/Integarray/dokuwiki (All lists will become available on the Integarray wiki: https://www.integralu19.org/index.php/Integarray/dokuwiki
  
 currently request an email to receive the information from ciamos@salud.unm.edu) currently request an email to receive the information from ciamos@salud.unm.edu)
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 Overall PCA for independent markers: Overall PCA for independent markers:
  
 +{{ :31949_ind_pc1_vs_pc2.png?500 |}}
  
 The QC steps prior to imputation were refined based on Chris’ suggestions. The QC steps prior to imputation were refined based on Chris’ suggestions.
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-No samples were dropped; all samples will be included in the imputation. +No samples were dropped; all samples will be included in the imputation, the marker lists of all steps can be found in file: {{ :integrarray_qc_guidelines_marker_list.xlsx |}}
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-· 735,370 markers in the original release (chr1–chr23) +
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-· 942 markers with ≥3 discordant calls among 149 duplicate pairs +
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-· 3,552 markers with p < 1×10⁻⁷ in controls +
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-· 2,052 markers with p < 1×10⁻¹² in cases +
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-· 23,112 markers with call rate < 0.95 +
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-· 27,119 total unique markers affected by filters (3), (4), (5), and (6)+
  
-· 708,672 markers remaining after removing the filtered markers+  *  **735,370** markers in the original release (chr1–chr23) 
 +  *  **942** markers with ≥3 discordant calls among 149 duplicate pairs, missing genotypes were not included 
 +  *  **3,552** markers with p < 1×10⁻⁷ in 14,537 unrelated caucasian controls 
 +  *  **2,052** markers with p < 1×10⁻¹² in 9895 unrelated caucasian cases 
 +  *  **23,112** markers with call rate < 0.95 
 +  *  **27,119** total unique markers affected by filters discordant calls, HWE and call rate 
 +  *  **708,672** markers remaining after removing the filtered markers 
 +  *  **632,677** markers retained after running the McCarthy Group Tool workflow against the TOPMed R3 reference panel
  
-· 615,894 markers retained after running the McCarthy Group Tool workflow against the TOPMed R3 reference panel 
integrarray_qc_guidelines.1765826704.txt.gz · Last modified: by 98.60.169.32