High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs

Walter, Nicole AR; Bottomly, Daniel; Laderas, Ted; Mooney, Michael A; Darakjian, Priscila; Searles, Robert P; Harrington, Christina A; McWeeney, Shannon K; Hitzemann, Robert; Buck, Kari J

doi:10.1186/1471-2164-10-379

BMC Genomics

Table 2 Missense B6 vs. D2 PARC SNPs discovered by custom HTS.

From: High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs

SNP identifier	Build 37 Chromosome 1 location (bp)	Gene	Ensembl Protein ID(ENSMUS)	Amino acid change	SIFT	PolyPhen
PARCsnp_1.00115¹	172981853	Fcgr3	P00000027964	D244E	tolerated	benign (A)
PARCsnp_1.00877¹	173088929	Mpz	P00000066701	T94A	tolerated	benign (A+S)
PARCsnp_1.01103^1,2	173126252	Pcp4l1	P00000049205	A40T	unknown	benign (A)
PARCsnp_1.01578^1,2,4	173186807	Adamts4	P00000006570	F574Y	tolerated	benign (A)
PARCsnp_1.01735¹	173214749	Usp21	P00000064002	C341R	tolerated	benign (A)
PARCsnp_1.02057¹	173268767	Nit1	P00000106927	L236R*	damaging	probably damaging (A)
PARCsnp_1.02149^1,4	173290449	Klhdc9	P00000056212	E115G*	tolerated	probably damaging (A)
PARCsnp_1.02252¹	173300263	Pvrl4	P00000106917	S12T	unknown	benign (A)
PARCsnp_1.02509⁴	173335292	Arhgap30	P00000059389	L458S	tolerated	benign (A)
PARCsnp_1.03202^3,4	173433896	Refbp2	P00000080242	R37S*	tolerated	possibly damaging (A)
PARCsnp_1.03321	173446982	novel	P00000048799	L84V	unknown	benign (A)
PARCsnp_1.14401	173503917	Cd244	P00000004829	T56K	tolerated	benign (A+S)
PARCsnp_1.03724¹	173503965	Cd244	P00000004829	D72G	tolerated	benign (A+S)
PARCsnp_1.03725¹	173504048	Cd244	P00000004829	K100Q	tolerated	benign (A+S)
PARCsnp_1.14405⁵	173504085	Cd244	P00000004829	T112I*	tolerated	probably damaging (A+S)
PARCsnp_1.03726	173504100	Cd244	P00000004829	K117R	tolerated	benign (A+S)
PARCsnp_1.03727^1,5	173504109	Cd244	P00000004829	N120T	tolerated	benign (A+S)
PARCsnp_1.03733^1,4	173504395	Cd244	P00000004829	I186T	tolerated	benign (A)
PARCsnp_1.03736	173504497	Cd244	P00000004829	S220L	tolerated	benign (A)
PARCsnp_1.14470	173510893	Cd244	P00000004829	S333F*	damaging	benign (A)
PARCsnp_1.03996¹	173537415	Ly9	P00000004827	G14S	tolerated	benign (A)
PARCsnp_1.05632^1,4	173826546	anon	P00000095074	T98A	unknown	benign (A)
PARCsnp_1.16162⁴	173826619	anon	P00000095074	G122E	unknown	benign (A)
PARCsnp_1.06789^1,2,3,5	174012752	Ncstn	P00000003550	S21F	tolerated	benign (A)
PARCsnp_1.06706^1,2,4	173996899	Ncstn	P00000003550	T678I*	tolerated	possibly damaging (A)
PARCsnp_1.06705^2,4	173996894	Ncstn	P00000003550	V680I	tolerated	benign (A)
PARCsnp_1.06990^1,2,4	174044893	Copa	P00000027833	S761T*	tolerated	possibly damaging (A)
PARCsnp_1.07003^1,2,3,5	174049099	Copa	P00000027833	N984S	tolerated	benign (A)
PARCsnp_1.07779⁴	174185185	Atp1a4	P00000007346	I74V	tolerated	benign (A)
PARCsnp_1.07693^1,4	174174231	Atp1a4	P00000007346	N476S	tolerated	benign (A)
PARCsnp_1.07664^1,4	174170189	Atp1a4	P00000007346	M546T	tolerated	benign (A)
PARCsnp_1.08379^1,2,4	174247711	Igsf8	P00000041232	H221R	tolerated	benign (A)
PARCsnp_1.08389^1,2	174248843	Igsf8	P00000041232	T489S	tolerated	benign (A)
PARCsnp_1.08838^1,2,4	174299836	Kcnj10	P00000054356	T262S	tolerated	benign (A)
PARCsnp_1.09831^1,4	174415000	Igsf9	P00000058275	H49R*	tolerated	possibly damaging (A)
PARCsnp_1.10673	174530187	Fcrl6	P00000091861	E11D	tolerated	benign (A)

Thirty-six of the seventy-six missense PARC SNPs between the D2 and B6 strains detected by custom HTS were not previously annotated in MPD. Confirmed SNPs are defined as those SNPs detected using two or more independent methods, including the Illumina and Applied Biosystems methods presented here. 30 of the 36 missense SNPs have been confirmed by one or more datasets. ¹confirmed by both Illumina and Applied Biosystems sequencing pipelines, ²confirmed by transcriptome sequencing (see Methods), ³confirmed by PCR directed sequencing [6], ⁴confirmed by realignment of Celera raw reads (see SNP Databases in Methods), or ⁵supported by imputed SNPs [24]. Ensembl protein IDs and respective amino acid differences are shown with the B6 amino acid residue indicated first and the D2 residue given last. Each amino acid change was assessed using two programs to determine whether or not the amino acid change is predicted to damage protein function. SIFT uses sequence conservation for predictions and PolyPhen predicts damaging changes using both multiple sequence alignments (A) and/or protein 3D structures (S).

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ISSN: 1471-2164

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