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how to determine the HLA LOH in DASH result file? #1

Open yinwei0108 opened 2 years ago

yinwei0108 commented 2 years ago

hi, I am confused about the DASH result file DASH.output.txt, freom this file how to determine the HLA LOH? eg the following result, which HLA is loss? Alleles DASH_deletion Secondary_check Confidence Flanking_region_LOH Adjusted_BAF AS_CoveragePurities Ploidies Percentage_Coverage Total_Coverage hla_a_02_06_01 False False 0.3748069405555725 1 0.052194658378937 1.0882472339075533 0.19 2 0.8125 2.0273821064147004 hla_a_24_02_01_01 False False 0.3748069405555725 1 0.052194658378937 0.9592126298487548 0.19 2 0.8125 2.0273821064147004 hla_b_13_01_01 False False 0.8209150433540344 1 0.08214848621750002 1.1628790893165517 0.19 2 0.9347826086956522 2.0504092899453887 hla_b_15_01_01_01 True False 0.8209150433540344 1 0.08214848621750002 0.8864985795735763 0.19 2 0.9347826086956522 2.0504092899453887 hla_c_03_04_01_02 False False 0.8672855496406555 1 0.048604364675094436 1.1014117145885538 0.19 2 0.8260869565217391 1.989508952895414 hla_c_04_01_01_01 True False 0.8672855496406555 1 0.048604364675094436 0.8068449476288686 0.19 2 0.8260869565217391 1.989508952895414

Personalis-DASH commented 2 years ago

The DASH_deletion column contains the predicted HLA LOH calls. If the row has a "True" value, that allele is predicted to be deleted. In your case, it looks like hla_b_15_01_01_01 and hla_c_04_01_01_01 are predicted to deleted.

yinwei0108 commented 2 years ago

@Personalis-DASH only the DASH_deletion column dtermine the HLA deletion? but both the paper of DASH and this result talk or give a value of Secondary_check, how to understand it, what does it mean when it is a "True" or "False"?

Personalis-DASH commented 2 years ago

The secondary_check is already included in the DASH_deletion result, so you don't need to worry about integrating it yourself.