17646 - PROC ALLLELE reports incorrect statistics with HAPLO=NONEHWD if individuals have missing alleles

Problem Note 17646: PROC ALLLELE reports incorrect statistics with HAPLO=NONEHWD if individuals have missing alleles

The correlation coefficient and chi-square goodness-of-fit test used to test markers for Hardy-Weinberg Equilibrium (HWE) are incorrectly computed in PROC ALLELE when the HAPLO=NONEHWD option is specified on the proc statement and individuals have missing alleles present.

When HAPLO=NONEHWD, the HWE coefficients that are used in the denominator of the correlation coefficient and chi-square test should be calculated using only individuals that are genotyped at both markers in the pair. Currently, all individuals genotyped at the single marker are being used.

There is no circumvention for this problem.

Select the Hot Fix tab in this note to access the hot fix for this issue.

Operating System and Release Information

Product Family	Product	System	Product Release		SAS Release
Product Family	Product	System	Reported	Fixed*	Reported	Fixed*
SAS System	SAS/Genetics	Microsoft Windows XP 64-bit Edition	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Microsoft Windows NT Workstation	2.2		9.1 TS1M3
		Microsoft Windows XP Professional	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Microsoft® Windows® for 64-Bit Itanium-based Systems	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Microsoft Windows Server 2003 Enterprise Edition	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Microsoft Windows Server 2003 Standard Edition	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Microsoft Windows 2000 Server	2.2		9.1 TS1M3
		Microsoft Windows Server 2003 Datacenter Edition	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Microsoft Windows 2000 Advanced Server	2.2		9.1 TS1M3
		Microsoft Windows 2000 Datacenter Server	2.2		9.1 TS1M3
		Microsoft Windows 2000 Professional	2.2		9.1 TS1M3
		64-bit Enabled Solaris	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		z/OS	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Linux	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		64-bit Enabled HP-UX	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Linux on Itanium	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		HP-UX IPF	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		OpenVMS Alpha	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		64-bit Enabled AIX	2.2	2.2	9.1 TS1M3	9.2 TS1M0
		Tru64 UNIX	2.2	2.2	9.1 TS1M3	9.2 TS1M0

* For software releases that are not yet generally available, the Fixed Release is the software release in which the problem is planned to be fixed.

A fix for SAS 9.1.3 (9.1 TS1M3) for this issue is available at:

http://www.sas.com/techsup/download/hotfix/e9_sbcs_prod_list.html#017646

Type:	Problem Note
Priority:	alert
Topic:	Analytics ==> Genetics SAS Reference ==> Procedures ==> ALLELE

Date Modified:	2008-12-04 10:38:52
Date Created:	2006-05-08 07:58:53

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Problem Note 17646: PROC ALLLELE reports incorrect statistics with HAPLO=NONEHWD if individuals have missing alleles

Operating System and Release Information