Table 2

Summary of all candidate genes.

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]

Dietz et al. BMC Neuroscience 2008 9:74   doi:10.1186/1471-2202-9-74