Table 1.
Schematics of the filtering steps used for WES-data. The procedure used to find heterozygous candidate variants in whole-exome data from four affected siblings and one unaffected sibling in a family with early onset AD (PED.25)
| Step | Criteria | Description | Number of variations passed | Genes with excluded variants (number of variants) |
|---|---|---|---|---|
| 1 | Rare and novel variants segregating with disease | CLC Genomic Workbench pipeline to extract shared variants in cases, not found in healthy sibling and with MAF < 1% in dbSNP138 | 1511 | for gene names, see Additional file 5: Table S3 |
| 2 | Non-synonymous or in splice-site region | Information annotated in CLC Genomic Workbench to include missense, nonsense, and variants in ± 2 nt of splice-site region | 109 | for gene names, see Additional file 5: Table S3 (1402) |
| 3 | Rare and novel variants in relevant populations | Excluded variants with MAF ≥ 1% found in either 1000G EUR, 1000G FIN, or in HBVDB Swedes/Danes | 74 |
RAD54L, MROH7, CENPF, TMEM63A, COCL6A6, TOPBP1, SLC17A4, TNXB, HLA-DPA1, CAPZA3, ABCC3, PRTN3, NOTCH2, PDE4DIP, PLEKHB2, MUC4, OR4C5, KCNJ12, TBC1D3, RP11-1407015.2, KRTAP-9, CDC27, EME1, SSC5D, C1orf94, XCR1, PIGZ, BTN1A1, TGFB2
(35) |
| 4 | Predicted to be deleterious, disease causing or to affect splicing | Alamut v.2.3 used for in-silico analysis of missense prediction to be either Deleterious (SIFT), to be Disease Causing (Mutation Taster) or being nonsense variations predicted to impact splicing by MaxEnt/NNSPLICE/HSF | 45 |
DMAP1, NBPF14, IGFN1, OBSCN, DNAH1, MUC4, TXNDC5, SLC17A3, MDC1, PRSS3, MUC6, PRR4, PRB1, C17orf74, CCDC144CP, MPP3, ZSCAN5A, SLC9B1P4, PLA2G3, C22orf42
(29) |
| 5 | Quality control of variant calls | Variants with low freq. (<20%), unbalanced F/R ratio (>0,1) and within repetitive sequence were removed | 13 |
SRGAP2, OBSCN, ANKRD36C, MUC4, FRG1, AP3S1, HLA-G, PFDN6, PRSS1, KMT2C, MUC6, SLC2A3, PRR4, PRB3, FAM186A, HNF1A, AC087499.7, RP11-1407O15.2, KRTAP1-3, KRTAP4-5, ANKFN1, ROCK1, CGB1, SPIB, FRG1B
(32) |
| 6 | Knowledge based prioritization | BioGSP to value expression profile and Ingenuity Pathway analysis to search for relevant processes | 7 |
PLSCR2, AOC2, AOC1, MYO7A, AQPR
(6) |
| 7 | Segregation analysis | Sanger sequencing in WES individuals and affected parent | 6 |
SLFNL1
(1) |
| 8 | Passed variations in genes: | LTF, MME, FAM221A, UBE4A, SORL1, KDM2B |