* The [ROSMAP WGS data](https://www.synapse.org/#!Synapse:syn10901595): 16 samples were identified that are either sex mismatches or discordant with previous array-based genotype data and recommended to be excluded. Samples are listed in [WGS_sample_QC_info](https://www.synapse.org/#!Synapse:syn12178037). Additional QC files can be found in the [QC files](https://www.synapse.org/#!Synapse:syn121779960 folder
* The [MSBB study](https://www.synapse.org/#!Synapse:syn3159438): 55 RNAseq, 8 WES, 15 WGS samples are recommended to be excluded or remapped to the correct donor. Samples are listed in [MSBB_RNAseq.WES.WGS_sample_QC_info](https://www.synapse.org/#!Synapse:syn12178047)
Created by Mette Peters Mette udube,
We (Mount Sinai group) performed a comprehensive genetic relationship alignment across different sequencing data types (WGS, WES and RNA-seq) generated from the same set of brains in MSBB cohort. If any sequencing sample showed some sort of mismatch, either a "suspicious" failure to match to samples from the same brain or a "spurious" match to samples from different brains given the sample annotation table, an iterative consensus voting procedure was carried out to try to recover (i.e. remap) the true brain identity of the problematic sample(s) identified. The samples whose brain identity was unidentifiable (ambiguous) were recommended to be excluded. The whole QC procedure iterated until converge (no more errors).
Hope this helps.
Minghui Thank you. Is it possible to get more information regarding how MSBB study samples were selected to be excluded or remapped? The first row in the table (syn12178047) seems like a match for sex, but no other information is provided and the sample is still listed as excluded. The description states: "For RNA-seq samples with documented matching WES, if the discordance rate between RNA-seq sample and its best corresponding exome sequence was more than 10%, the sample was removed." Is this the case for these samples? Was the same process done using the WGS data as well?