Rgcs1, a dominant QTL that affects retinal ganglion cell death after optic nerve crush in mice

Dietz, Joel A; Li, Yan; Chung, Lisa M; Yandell, Brian S; Schlamp, Cassandra L; Nickells, Robert W

doi:10.1186/1471-2202-9-74

BMC Neuroscience

Table 2 Summary of all candidate genes.

From: Rgcs1, a dominant QTL that affects retinal ganglion cell death after optic nerve crush in mice

Gene Name	Chromosome Position (starting bp)	Retinal Expression	Coding Region SNP^c	Strain Association^d	Role in Neurodegeneration
Pcdh7	58006337	GCL enriched^a,b	No	N/A	Unknown
Tlr1	65203969	Confirmed^b	Yes	Possible	Immune Modulation^e
Tlr6	65232241	Confirmed^b	Yes	Yes	Immune Modulation^e
Uchl1	66955376	GCL enriched^a,b	No	N/A	eQTL Susceptibility Allele^f
Sparcl1	104319413	GCL enriched^a,b	Yes	Possible	Possible Glial Activation^g
Cplx1	108760431	GCL enriched^a,b	No	N/A	2° Degeneration^h
Hspb8	116669490	Confirmed^b	No	N/A	Susceptibility Alleleⁱ

The chromosomal position of each gene is shown, along with a short summary of how each gene scored in the different criteria for identifying candidate genes.
^aIdentified from microarray expression profiles.
^bThe expression of each candidate gene was confirmed in the mouse retina using reverse transcriptase-PCR amplification of a portion of its cDNA (data not shown).
^cSingle nucleotide polymorphism (SNP) analysis was conducted in silico using sequence information available on the MGI data base. SNPs that resulted in coding region changes between DBA/2J and BALB/cByJ mice were examined.
^dCoding region SNPs between DBA/2J and BALB/cByJ mice were compared to reference strains if sequence data were available. Reference strains included 129X1/SVJ and C57Bl/6J as resistant strains comparable to DBA/2J mice, and NOD/LtJ and C3H/HeJ as susceptible strains comparable to BALB/cByJ mice. Intermediate strains included A/J (as a likely resistant strain) and NZB/BINJ (as a likely susceptible strain). For genes showing a SNP difference, if the same SNP was noted in the reference strains it was scored as showing a positive strain association. A possible strain association was recorded if sequence data was limited to only a resistant or susceptible reference strain, or the intermediate strains showed the predicted strain association, but there was not data available for the reference strains. If no SNP was noted, the strain association analysis was not applicable (N/A).
^e[31, 33].
^f [34–36].
^g[37].
^h[40].
ⁱ[45]

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ISSN: 1471-2202

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