Reporting of Human Genome Epidemiology (HuGE) association studies: An empirical assessment

Yesupriya, Ajay; Evangelou, Evangelos; Kavvoura, Fotini K; Patsopoulos, Nikolaos A; Clyne, Melinda; Walsh, Matthew C; Lin, Bruce K; Yu, Wei; Gwinn, Marta; Ioannidis, John PA; Khoury, Muin J

doi:10.1186/1471-2288-8-31

BMC Medical Research Methodology

Table 7 Comparison of the reporting characteristics of HuGE articles from two time periods (2001–2003 vs. 2006)

From: Reporting of Human Genome Epidemiology (HuGE) association studies: An empirical assessment

	Published from 2001–2003		Published in 2006
Reporting characteristic	Count	Percent	Count	Percent	P-Value^a
Basic descriptive items
Number of study participants
< 100	49	15.6	5	17.9	0.90
100–499	190	60.3	16	57.1
500–999	47	14.9	4	14.3
>= 1000	29	9.2	3	10.7
Number of genes analyzed
1	188	59.7	21	75.0	0.12
2	71	22.5	4	14.3
>= 3	56	17.8	3	10.7
Number of genetic variants analyzed
1	114	36.2	10	35.7	0.29
2	85	27.0	4	14.3
3	56	17.8	6	21.4
4	21	6.6	1	3.6
>= 5	39	12.4	7	25.0
Number of environmental factors examined in gene-environment interactions
1	34	70.8	1	50.0	0.26
2	10	20.8	1	50.0
>= 3	4	8.4	0	0.0
Items applicable to all articles that were addressed in less than 50% of the 2001–2003 HuGE articles
Reported the available power of the study
No	275	87.3	20	71.4	0.03
Yes	40	12.7	8	28.6
Explicitly stated the use of unrelated study participants
No	259	82.2	18	64.3	0.03
Yes	56	17.8	10	35.7
Reported that genotyping results were validated using duplicate samples
No	293	93.0	22	78.6	0.02
Yes	22	7.0	6	21.4
Reported that genotyping results were validated using a different method
No	284	90.2	24	85.7	0.32
Yes	31	9.8	4	14.3
Reported that the evaluation of the genetic test was blind to outcomes or phenotypes
Blind	35	11.1	3	10.7	0.62
Unclear	280	88.9	25	89.3
Reported that the evaluation of the outcomes or phenotypes was blind to the genetic test
Blind	12	3.8	2	7.1	0.32
Unclear	303	96.2	26	92.9
Reported that individuals were excluded from the original group(s) of study participants
No	278	88.2	26	92.9	0.86
Yes	37	11.8	2	7.1
Reported that several samples could not be genotyped
No	266	84.4	23	82.1	0.46
Yes	49	15.6	5	17.9
Reported that unlinked genetic markers were used to identify population stratification
No	313	99.4	28	100.0	1.00
Yes	2	0.6	0	0.0
Reported that all genetic variants were examined for Hardy-Weinberg equilibrium
No	164	52.1	12	42.9	0.23
Yes	151	47.9	16	57.1

^a P-values were determined from two-sided Mann-Whitney U tests for the basic descriptive items and one sided Fisher's Exact Tests for the items that were reported in less than 50% of the 2001–2003 articles.

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ISSN: 1471-2288

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