BMC Proceedings

Table 2 Feature selection

From: Using LASSO regression to detect predictive aggregate effects in genetic studies

Model type	Model 1						Model 3
	Gene	SNP	Count^a	MAF^b	Causal^c		Gene	SNP	Count^a	MAF^b	Causal^c
Gene only	FLT1	C13S523	35	0.0667	Y		FLT1	C13S523	71	0.0667	Y
	ADAMTS7	C15S3360	22	0.0029	N		SRPR	C11S6885	63	0.0014	N
	TG	C8S4379	17	0.0050	N		TG	C8S4379	61	0.0050	N
	MDN1	C6S4146	15	0.0050	N		RPA3	C7S297	58	0.0007	N
	GOLGA1	C9S4013	13	0.0308	N		LAMB3	C1S10178	54	0.0007	N
	FLT1	C13S522	12	0.0280	Y		RPL27	C17S2981	52	0.0007	N
Gene restricted	FLT1	C13S523	19	0.0667	Y		FLT1	C13S523	44	0.0667	Y
	TEX14	C17S3819	9	0.0043	N		FLT1	C13S522	24	0.0280	Y
	FLT1	C13S522	8	0.0280	Y		CYP3A43	C7S2324	21	0.0976	N
	UBA3	C3S2197	7	0.0108	N		TG	C8S4379	18	0.0050	N
	GOLGA1	C9S4013	7	0.0308	N		PRKCA	C17S4578	16	0.1664	Y
	CYP3A43	C7S2324	7	0.0976	N		PIK3C2B	C1S9189	15	0.0065	Y
Combined	Age	Age	200	NA	Y		Age	Age	200	NA	Y
	Smoke	Smoke	163	NA	Y		Smoke	Smoke	185	NA	Y
	FLT1	C13S523	49	0.0667	Y		FLT1	C13S523	81	0.0667	Y
	FLT1	C13S522	16	0.0280	Y		FLT1	C13S522	34	0.0280	Y
	PIK3C3	C18S2492	7	0.0172	Y		PIK3C3	C18S2492	18	0.0172	Y
	HFE	C6S853	3	0.0036	N		PRKCA	C17S4578	8	0.1664	Y
	ARNT	C1S6533	3	0.0115	Y		ARNT	C1S6533	8	0.0115	Y
	ACP1	C2S1	2	0.0093	N		UBA3	C3S2197	7	0.0108	N
Combined restricted	Age	Age	200	NA	Y		Age	Age	200	NA	Y
	Smoke	Smoke	163	NA	Y		Smoke	Smoke	180	NA	Y
	FLT1	C13S523	49	0.0667	Y		FLT1	C13S523	75	0.0667	Y
	FLT1	C13S522	17	0.0280	Y		FLT1	C13S522	32	0.0280	Y
	PIK3C3	C18S2492	7	0.0172	Y		PIK3C3	C18S2492	17	0.0172	Y
	ARNT	C1S6533	3	0.0115	Y		UBA3	C3S2197	6	0.0108	N
	LARGE	C22S1540	3	0.0201	N		ARNT	C1S6533	6	0.0115	Y
	MMS19	C10S4869	3	0.0050	N		KDR	C4S1861	5	0.0022	Y

^a Number of times a given variable was observed in four out of five trained models.
^b Minor allele frequency.
^c Variables used to determine disease risk by the GAW17 simulators.
The top most frequent variables occurred in at least four out of five trained models for models 1 and 3. All models were run for the 200 simulation data sets.

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ISSN: 1753-6561

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