Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

Mullen, Michael P; Creevey, Christopher J; Berry, Donagh P; McCabe, Matt S; Magee, David A; Howard, Dawn J; Killeen, Aideen P; Park, Stephen D; McGettigan, Paul A; Lucy, Matt C; MacHugh, David E; Waters, Sinead M

doi:10.1186/1471-2164-13-16

Table 4 Comparison between allele frequencies generated using Sequenom^® MassARRAY and Illumina GAIIx technologies.

From: Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

EntrezGene ID	Chr.	SNP name¹	Position	Allele sub.²	Allele frequency in low CIV pool³		P value⁴	Allele frequency in high CIV pool³		P value⁴	Reference⁵
					Actual	NGS		Actual	NGS
		S555G	33897071	T > C	0.19	0.15	1.00	0.12	0.10	1.00	AF140284
		H545	33897099	A > G	0.34	0.28	0.96	0.15	0.18	1.00	AF140284
		A536T	33897128	C > T	0.13	0.15	1.00	0.02	0.00	1.00	AF140284
		N528T	33897151	T > G	0.21	0.22	1.00	0.12	0.10	1.00	AM161140
		GHR76	33897252	A > G	0.13	0.14	1.00	0.02	0.00	1.00	n/a
		F279Y	33915503	A > T	0.00	0.00	1.00	0.09	0.09	1.00	AM161140
		GHR19.1	33994639	G > T	0.62	0.65	1.00	0.47	0.29	0.23	rs109702942
		GHR18.2	33995251	G > C	0.07	0.09	1.00	0.00	0.00	1.00	n/a
		AF126288:g.149	34086084	C > T	0.69	0.73	1.00	0.31	0.29	1.00	AF126288
GHR	20	GHR9.1	34101240	C > T	0.05	0.00	0.96	0.37	0.33	1.00	rs110979028
		GHR3.3	34166627	A > G	0.08	0.12	1.00	0.43	0.39	1.00	n/a
		GHR3.2	34166731	A > G	0.09	0.13	1.00	0.43	0.31	0.96	n/a
		GHR3.1	34166898	T > C	0.09	0.00	0.23	0.42	0.33	0.96	n/a
		GHR2.6	34166944	C > T	0.09	0.00	0.22	0.42	0.38	1.00	rs109825954
		GHR2.5	34166970	A > G	0.09	0.00	0.23	0.42	0.36	1.00	n/a
		GHR2.4	34166982	A > C	0.09	0.00	0.22	0.43	0.33	0.96	n/a
		GHR2.3	34167025	C > T	0.09	0.00	0.23	0.42	0.37	1.00	n/a
		GHR2.2	34167126	G > A	0.09	0.09	1.00	0.43	0.35	1.00	n/a
		GHR2.1	34167240	C > T	0.09	0.00	0.13	0.44	0.52	1.00	n/a
		GH19	49657225	G > A	0.90	0.86	1.00	0.84	0.91	1.00	rs41923481
		GH18	49657293	G > A	0.92	0.82	1.00	0.92	0.90	1.00	rs196003433
		GH17	49657371	C > G	0.92	1.00	1.00	0.89	1.00	1.00	rs41923483
		2291	49660125	T > G	0.08	0.00	0.13	0.12	0.08	1.00	n/a
		2141	49660275	G > C	0.33	0.36	1.00	0.09	0.11	1.00	rs41923484
		GH6	49660469	A > C	0.08	0.00	0.96	0.12	0.12	1.00	rs196003424
		GH38	49693278	G > A	0.33	0.21	1.00	0.59	0.60	1.00	rs41923525
GH1	19	GH37	49693285	C > G	0.29	0.15	0.96	0.54	0.58	1.00	rs41923524
		GH36	49693316	G > C	0.29	0.40	1.00	0.52	0.38	1.00	rs41923523
		GH35	49693328	G > A	0.30	0.35	1.00	0.55	0.29	0.96	rs41923522
		GH34	49693374	C > G	0.34	0.33	1.00	0.61	0.53	1.00	rs41923521
		GH32	49693442	A > G	0.67	0.58	1.00	0.39	0.37	1.00	rs196301608
		GH31	49693460	C > T	0.67	0.62	1.00	0.39	0.28	1.00	rs196003442
		GH30	49693512	A > G	0.66	0.65	1.00	0.38	0.38	1.00	rs196003441
		GH29	49693686	C > T	0.50	0.26	0.36	0.50	0.64	0.96	rs41923520
		rs29012855	71150007	C > T	0.99	1.00	1.00	0.90	0.93	1.00	rs29012855
		IGF1i3	71175747	T > C	0.17	0.24	0.95	0.01	0.00	1.00	rs109557731
IGF1	5	IGF1i2	71175753	A > G	0.49	0.46	1.00	0.25	0.15	0.70	rs109227434
		IGF1i1	71176219	A > T	0.26	0.16	1.00	0.37	0.25	1.00	rs110076130
		AF017143	71198324	G > A	0.35	0.26	0.96	0.62	0.76	0.92	AF017143
IGF2	29	IGF2_B_6646	51250879	A > G	0.40	0.40	1.00	0.65	0.47	0.83	rs42196909
		IGF2R_D_41515	100112956	A > G	0.87	0.79	1.00	0.87	0.87	1.00	rs41623543
IGF2R	9	IGF2R_D_41092	100113379	G > A	0.63	0.65	1.00	0.77	0.47	0.22	rs41623544
		IGF2R:g.86262	100134604	G > A	0.86	0.76	0.73	0.86	1.00	0.62	n/a

¹: SNP details according to previous studies [4, 5, 7, 31, 32]; ²: Reported from the forward strand; ³: Allele frequencies represents second allele; ⁴: Benjamini and Hochberg corrected P values; ⁵:Genbank accession or dbSNP reference (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/projects/SNP/ accessed 9^th September 2011).

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