UHS4 dbGaP submission

[jaamarks]

Dear Eric,
Thank you for your resubmission of subject consent and subject phenotype files. I checked your phenotype files and our QC test has identified:
dbGaP_phenotypeDS_20191211:
ERROR: 5 subjects have SEX conflicts submitted in version 1 and version 2 of the phs454.
        Subject 'HHG1973' (dbGaP ID 575872): Sex = 1 in version 1, Sex = 2 in version 2;
        Subject 'HHG4751' (dbGaP ID 577134): Sex = 1 in version 1, Sex = 2 in version 2;
        Subject 'HHG6687' (dbGaP ID 578027): Sex = 1 in version 1, Sex = 2 in version 2;
        Subject 'HHG7140' (dbGaP ID 578252): Sex = 2 in version 1, Sex = 1 in verslion2;
        Subject 'HHG7939' (dbGaP ID 578591): Sex = 1 in version 1, Sex = 2 in version 2.
Please check sex of these subjects in the subject phenotype data set [dbGaP_phenotypeDS_20191211] and let me know if you intensely changed sex of these subjects between version 1 and version 2 of the phs452.
Please answer to me as soon as possible.
Please keep in mind that because according to your pedigree file your subjects do not have relationship we removed your pedigree file from your study processing.
Please find you study status at https://www.ncbi.nlm.nih.gov/gap/study/status/6601. 
Regards,
Natasha

Version 002 of phenotype files

dbGaP_phenotypeDD_20191211.xlsx
dbGaP_phenotypeDS_20191211.txt

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Issues

• some entries are blank. They need to be filled in with the missing data entry -99999.
• need to make missing-entry-numbers consistent. Some have numbers other than -99999, like -8,-2,-99, etc.
• 5 sex discrepant samples (see quoted at the top). Note that 1=male and 2=female.
• some data are not filled in, but we actually do have data for them—either in the master phenotype file: s3://rti-heroin/hiv_all_merged_with_uhs_all_phenotype_data_08282017.csv.gz, in the GWAS phenotype, or in the observed genotype data.

[jaamarks]

5 Sex Discrepant Samples

dbGaP_phenotypeDS_03292013.txt

This sheet was found at:
//RTPNFIL02/eojohnson/HIV/hiv_data/UHS/UHS dbGaP submission/FinalPhenotypeFiles_dbGaP/Updated_030413/Updated_032913/dbGaP_phenotypeDS_03292013.txt

Previous Submission:

subjid	sampid	consent	affection_status	hivstat	ViralLoad_cperml	ViralLoad_Log10	sex	gwassex	race	age	age_cat	year	year_cat	lca_groupá	mpartners	stis	anal	needleshare	sexwork	site	cluster	final_analysis
HHG4751	328952	1	1	1	35000	4.54	1	1	1	44	1	1998	2	3	0	1	0	0	0	2	271	1
HHG6687	407014	1	2	0	-99999	-99999	1	-2	2	37	0	1994	1	1	0	-99999	0	-99999	1	2	-99999	1
HHG7140	513323	1	1	1	1060	3.03	2	2	2	42	1	1992	1	1	0	0	0	-99999	1	2	220	1
HHG7939	448818	1	2	0	-99999	-99999	1	-2	2	38	1	1997	2	2	0	0	0	0	0	2	-99999	1

• HHG1973 not in this original submission.
• 1=male, 2=female
• -2 for gwassex—this is not defined in the dictionary file //RTPNFIL02/eojohnson/HIV/hiv_data/UHS/UHS dbGaP submission/FinalPhenotypeFiles_dbGaP/Updated_030413/dbGaP_phenotypeDD_02072013.txt

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2020 Submission

subjid	hivstat	age_hiv	viralload_cperml	viralload_log10	sex_selfreport	gwassex	ancestry_selfreport	age	surveyyear	lca_group	mpartners	stis	anal	needleshare	sexwork	site	heroin_ever	heroin_ever_inj	opioid_ever	opioid_ever_inj	totopioid_ever	heroin_age_ons	opioid_age_ons	totopioid_age_ons	heroin_inj_30d	heroin_non_30d	opioid_inj_30d	opioid_non_30d	totopioid_inj_30d	totopioid_non_30d	totopioid_tot_30d	heroin_case	opioid_case	totopioid_case	inj_ever	inj_freq	inj_case	inj_age_ons	coc_ever	coc_ever_inj	amphet_ever	amphet_ever_inj	sed_ever	sed_ever_inj	mj_ever	coc_age_ons	amphet_age_ons	sed_age_ons	mj_age_ons	cocaine_inj_30d	cocaine_non_30d	totcoc_30d	amphet_inj_30d	amphet_non_30d	totamphet_30d	mj_30d	totcoc_case	totamphet_case	mj_case
HHG4751	1	43	35000	5	2	1	1	43	1998	3	0	1	0	0	0	1	1	1	1	1	1	19	20	19	49	0	0		49	0	49	1	0	1	1	57	1	19	1	1	1	1	1	-8	1	19	-99999	-99999	-99999	0	0	0	8	3	11		0	1
HHG6687	0	-99999	-99999	-99999	2	-99999	2	36	1994	1	0	-99999	0	-99999	1	1	1	1	-8	-8	-8	-8	-8	-8	30	15	0	0	30	15	45	1	0	1	1	30	1		1	-8	-8	-8	-8	-8	1	-99999	-99999	-99999	14	0	45	45	0	0	0	1	1	0	0
HHG7140	1	45	1060	3	1	2	2	45	1992	1	0	0	0	-99999	1	1	1	1	1	1	1	21		21	75	0	0		75	0	75	1	0	1	1	125	1	21	1	1	1	1	-8	-8	-99999	30	-99999	-99999	-99999	0	30	30	50	0	50		1	1
HHG7939	0	-99999	-99999	-99999	2	-99999	2	36	1997	2	0	0	0	0	0	1	1	1	-8	-8	-8	-8	-8	-8	120	30	0	0	120	30	150	1	0	1	1	120	1		1	-8	-8	-8	-8	-8	1	-99999	-99999	-99999	12	0	20	20	0	0	0	99	1	0	1
HHG1973	0	-99999	-99999	-99999	2	-99999	2	41	1993	1	1	1	0	0	1	2	1	1	0	0	1	31		31	24	0	0	0	24	0	24	1	0	1	1	24	1	32	1	0	0	0	0	0	1	33			28	0	27	27	0	0	0		1	0

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In Latest GWAS

HHG4751 328952@1054755694
HHG6687 407014@1054753316
HHG7140 513323@1054752755
HHG7939 448818@1054697882
HHG1973 942966@1054697675

iid	hiv	age	gender	PC1	PC9	PC10
328952@1054755694_328952@1054755694	1	43	1	-0.002	0.0132	5.00E-04
407014@1054753316_407014@1054753316	0	36	1	0.0111	0.0031	0.001
513323@1054752755_513323@1054752755	1	45	0	-0.011	0.0189	0.006
448818@1054697882_448818@1054697882	0	36	1	0.0079	-0.0096	-0.0077
942966@1054697675_942966@1054697675	0	41	1	0.0048	0.0019	-5.00E-04

• 0 female, 1 male
• all in the AA GWAS

[jaamarks]

2020 Submission

subjid	hivstat	age_hiv	viralload_cperml	viralload_log10	sex_selfreport	gwassex	ancestry_selfreport	age	surveyyear	lca_group	mpartners	stis	anal	needleshare	sexwork	site	heroin_ever	heroin_ever_inj	opioid_ever	opioid_ever_inj	totopioid_ever	heroin_age_ons	opioid_age_ons	totopioid_age_ons	heroin_inj_30d	heroin_non_30d	opioid_inj_30d	opioid_non_30d	totopioid_inj_30d	totopioid_non_30d	totopioid_tot_30d	heroin_case	opioid_case	totopioid_case	inj_ever	inj_freq	inj_case	inj_age_ons	coc_ever	coc_ever_inj	amphet_ever	amphet_ever_inj	sed_ever	sed_ever_inj	mj_ever	coc_age_ons	amphet_age_ons	sed_age_ons	mj_age_ons	cocaine_inj_30d	cocaine_non_30d	totcoc_30d	amphet_inj_30d	amphet_non_30d	totamphet_30d	mj_30d	totcoc_case	totamphet_case	mj_case
HHG4751	1	43	35000	5	2	1	1	43	1998	3	0	1	0	0	0	1	1	1	1	1	1	19	20	19	49	0	0		49	0	49	1	0	1	1	57	1	19	1	1	1	1	1	-8	1	19	-99999	-99999	-99999	0	0	0	8	3	11		0	1
HHG6687	0	-99999	-99999	-99999	2	-99999	2	36	1994	1	0	-99999	0	-99999	1	1	1	1	-8	-8	-8	-8	-8	-8	30	15	0	0	30	15	45	1	0	1	1	30	1		1	-8	-8	-8	-8	-8	1	-99999	-99999	-99999	14	0	45	45	0	0	0	1	1	0	0
HHG7140	1	45	1060	3	1	2	2	45	1992	1	0	0	0	-99999	1	1	1	1	1	1	1	21		21	75	0	0		75	0	75	1	0	1	1	125	1	21	1	1	1	1	-8	-8	-99999	30	-99999	-99999	-99999	0	30	30	50	0	50		1	1
HHG7939	0	-99999	-99999	-99999	2	-99999	2	36	1997	2	0	0	0	0	0	1	1	1	-8	-8	-8	-8	-8	-8	120	30	0	0	120	30	150	1	0	1	1	120	1		1	-8	-8	-8	-8	-8	1	-99999	-99999	-99999	12	0	20	20	0	0	0	99	1	0	1
HHG1973	0	-99999	-99999	-99999	2	-99999	2	41	1993	1	1	1	0	0	1	2	1	1	0	0	1	31		31	24	0	0	0	24	0	24	1	0	1	1	24	1	32	1	0	0	0	0	0	1	33			28	0	27	27	0	0	0		1	0

In GWAS

HHG4751 328952@1054755694
HHG6687 407014@1054753316
HHG7140 513323@1054752755
HHG7939 448818@1054697882
HHG1973 942966@1054697675

iid	hiv	age	gender	PC1	PC9	PC10
328952@1054755694_328952@1054755694	1	43	1	-0.002	0.0132	5.00E-04
407014@1054753316_407014@1054753316	0	36	1	0.0111	0.0031	0.001
513323@1054752755_513323@1054752755	1	45	0	-0.011	0.0189	0.006
448818@1054697882_448818@1054697882	0	36	1	0.0079	-0.0096	-0.0077
942966@1054697675_942966@1054697675	0	41	1	0.0048	0.0019	-5.00E-04

• 0 female, 1 male
• all in the AA GWAS

[jaamarks]

Summary of UHS sex issues

20200122_uhs_problematic_sex_n34.xlsx