# 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.


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