Mosaic chromosomal alterations (mCA)

This page has been last updated for R11.

Sandbox directory

Mosaic chromosomal alterations (mCAs) are available in the following Sandbox directory:

/finngen/library-red/finngen_R[RELEASE]/mca_1.0/

Data files

Two types of files are available for samples included in mCA calling:

• Basic information file

• Detailed information file

The mCA calling was done with MoChA (https://github.com/freeseek/mocha). For QC, we removed samples with call_rate lower than 0.97 and baf_auto greater than 0.03 and CNV calls likely to be germline.

Basic information file

Basic information of Affymetrix samples included in mCA calling, computed gender, genotype calling rate, and phased BAF, is available in the following file:

data/finngen_R11_stats.tsv

The number of samples in Data Release 11 (R11) was 395,716. Legacy samples are excluded since raw intensity data is not available for them.

Detailed information file

Detailed information of Affymetrix samples included in mCA calling, computed gender, chromosome, beginning/end base pair position, whether or not the call extends to p-arm/q-arm, BAF deviation, LRR, number of (heterozygous sites) used for the call, mCA type, and cell fraction, is available in the following file:

data/finngen_R11_mca.tsv

The number of samples in Data Release 11 (R11) was 116,401.

Further information

For more details regarding mCA calling and QC, see:

(1) Liu, A., Genovese, G., Zhao, Y., Pirinen, M., Zekavat, M.M., Kentistou, K., Yang, Z., Yu, K., Vlasschaert, C., Liu, X. and Brown, D.W., 2023. Population analyses of mosaic X chromosome loss identify genetic drivers and widespread signatures of cellular selection. medRxiv, pp.2023-01.

(2) Zekavat, S.M., Lin, S.H., Bick, A.G., Liu, A., Paruchuri, K., Wang, C., Uddin, M.M., Ye, Y., Yu, Z., Liu, X. and Kamatani, Y., 2021. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nature medicine, 27(6), pp.1012-1024.

(3) Koskela, J.T., Häppölä, P., Liu, A., FinnGen, Partanen, J., Genovese, G., Artomov, M., Myllymäki, M.N., Kanai, M., Zhou, W. and Karjalainen, J.M., 2021. Genetic variant in SPDL1 reveals novel mechanism linking pulmonary fibrosis risk and cancer protection. medRxiv, pp.2021-05.