4 Results
4.2.3.4 Secondary MIP design for Rescuing the Capture of MIPseq Targets
An iterative redesign was performed for target regions of non-improvable low performing MIPs (after balancing), which affected 80,726 bp of MIP target regions. After the secondary design, QC and filtering, 331 additional MIPs were obtained (see MIPs in appendix, p. 155), which covered 18,548 bp (23.0%), and added to the rebalanced MIPs pool at one standard MIP concentration.
4.2.3.5 Evaluation of the Rebalanced MIPs Pool
MIPseq libraries were prepared for 46 samples using either the balanced or rebalanced MIPs pool.
The libraries were sequenced on HiSeq 2500 machines. The coverage distributions were compared for the MIPs’ targets between the balanced and rebalanced MIPs pool (Figure 10, p. 60). By visual inspection, the shape did not differ (Figure 10, A and B2, p. 60). But, as expected, the off-target ratio
4.2 Targeted Sequencing of RLS Candidate Genes
was higher in the MIPseq data of the rebalanced MIPs pool (on average per individual 21.26% vs 17.43%, p = 3.752E-06, two sided t-test). To compare the performance of the two MIPs pools in more detail, the effect of the two distinct sequencer machine runs were removed. Therefore, the MIPs’ targets’ coverages were corrected to remove differences in the general sequencer output amount of the two machine runs. Then the MIPs’ targets were counted that exceeded 10X coverage (as the lowest threshold for variant calling) and summed for all individuals. As a result, the rebalanced MIPs pool led to a slightly better performance compared to the balanced MIPs pool (412,750 targets vs 409,163 targets and 8,973 targets/person vs 8,895 targets/person, respectively).
The odds were calculated of the MIPs’ targets that were suitable and not suitable for the calling of genetic variants, respectively, and they were lower for the rebalanced MIPs pool compared to the balanced MIPs pool (4.00 vs 4.47, respectively). To sum up, the rebalanced MIPs pool enabled the acquisition of more data of interest with the same sequencer setup and it was selected for further experiments.
4 Results
Figure 8: Exemplary bar plots of MIPs’ reads distributed over hg19 decoy reference genome: A) MIP with many off-target reads and B) normal MIP. (The MIPs’ names are indicated in grey.)
M 0 0 7 6 4 _ A S T N 2 _ M IP 6 9 M 0 0 7 6 4 _ P LX N A 2 _ M IP 1 5 8
A) B)
4.2 Targeted Sequencing of RLS Candidate Genes
Figure 9: Total coverage distribution of MIPs’ targets after balancing: Shown are the log10 of the minimum base coverages of the MIPs’ targets, summed over all sequenced individuals. A) Naïve MIPs pool, B1) MIPs pool after balancing in order of A), B2) MIPs pool after balancing (reordered)
4 Results
Figure 10: Total coverage distribution of MIPs’ targets after rebalancing: Shown are the log10 of the minimum base coverages of the MIPs’ targets, summed over all sequenced individuals. A) balanced MIPs pool, B1) rebalanced MIPs pool (without MIPs’ targets from the 2ary design, in order of A), B2) as B1 (reordered), B3) as B2 (with MIPs’ targets from the 2ary design in green).
4.2 Targeted Sequencing of RLS Candidate Genes
4.2.4 MIPseq of a Case-Control Cohort Using the Rebalanced MIPs Pool 4.2.4.1 Power Analysis
The median analytic power was calculated for comparing differences in cumulative MAF [411]
between 750 RLS cases and 750 controls under a variety of scenarios (100 replicates, results in Table 22, p. 62). No power estimates were obtained for 2 of 84 genes (CASC16 and LAMA1, which were not part of the population model used for the power analysis). Eight genes showed a power greater 80%
in at least one scenario: TANC1, SETBP1, COL6A6, PTPRM, MYT1, ASTN2, EYA2, and PLXNA2. The power would be substantially higher with 5,000 cases and 5,000 controls, and 57 genes showed a power greater 80% in at least one scenario. Of those, 7 genes showed a power of at least 80% in all scenarios. Table 23 (p. 65) shows the respective results of this power analysis.
4.2.4.2 Capacity Estimation for HiSeq 4000 Sequencers
The optimal HiSeq 4000 setup was determined based on a simulated 372-plex MIPseq library (Figure 11). The optimum number of lanes was heuristically determined to be 6; a plateau was reached for the average number of targets exceeding a minimal coverage threshold suitable for calling variants.
Figure 11: Average number of MIPseq targets per person with a coverage suitable for variant calling as a function of HiSeq 4000 lanes: A 372-plex MIPseq library was simulated to have been sequenced on an increasing number of HiSeq 4000 lanes, which was based on the MIPseq output of the HiSeq 2500 rebalancing run (sample size 46).
62 4 Results Table 22: Power analysis for gene-level tests of 82 genes and sample size 1,500: The median power is shown from 100 replicates (of gene models). CASC16 and LAMA1 were not included in the power analysis. The genes were ordered according to power over all scenarios. Green = genes with median power ≥ 0.8, OR = upper bound for OR of detrimental variants, causal = proportion of RLS causing variants in detrimental variants, α = type I error rate (for 100 and 20,000 independent null hypotheses, respectively).
Gene
Prevalence = 5% Prevalence = 10%
75% causal 100% causal 75% causal 100% causal
α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 TANC1 0.62 0.29 0.97 0.50 0.95 0.81 1.00 0.99 0.75 0.04 0.49 0.33 0.98 0.54 1.00 0.77 SETBP1 0.30 0.02 0.85 0.19 0.93 0.26 0.98 0.77 0.25 0.10 0.86 0.23 0.80 0.28 0.99 0.77 COL6A6 0.03 0.09 0.33 0.20 0.78 0.08 0.98 0.71 0.10 0.02 0.69 0.09 0.74 0.66 0.93 0.47 PTPRM 0.05 0.01 0.32 0.27 0.68 0.29 0.96 0.44 0.27 0.03 0.41 0.15 0.40 0.08 0.85 0.35 MYT1 0.22 0.01 0.49 0.19 0.40 0.09 0.91 0.36 0.07 0.00 0.31 0.10 0.46 0.07 0.87 0.40 ASTN2 0.19 0.00 0.51 0.08 0.36 0.08 0.77 0.45 0.05 0.01 0.50 0.19 0.53 0.06 0.80 0.31 EYA2 0.07 0.01 0.75 0.14 0.43 0.04 0.77 0.29 0.11 0.01 0.15 0.28 0.39 0.04 0.66 0.22 PLXNA2 0.01 0.00 0.58 0.18 0.47 0.08 0.81 0.43 0.00 0.00 0.14 0.08 0.27 0.02 0.78 0.25 COL20A1 0.03 0.01 0.49 0.11 0.24 0.03 0.77 0.30 0.02 0.01 0.22 0.09 0.21 0.03 0.52 0.25 MDGA1 0.13 0.00 0.41 0.04 0.23 0.04 0.62 0.22 0.02 0.00 0.23 0.02 0.16 0.02 0.38 0.12 IQCH 0.01 0.00 0.17 0.08 0.18 0.04 0.65 0.11 0.02 0.00 0.12 0.05 0.14 0.01 0.64 0.21 TOX3 0.00 0.00 0.21 0.05 0.10 0.02 0.52 0.15 0.06 0.00 0.25 0.35 0.22 0.04 0.22 0.20 RIMS2 0.05 0.00 0.10 0.08 0.11 0.03 0.60 0.27 0.00 0.00 0.07 0.09 0.08 0.01 0.52 0.21 CORO6 0.00 0.01 0.15 0.15 0.04 0.02 0.67 0.26 0.00 0.00 0.12 0.02 0.13 0.02 0.52 0.05 ADAM22 0.01 0.02 0.12 0.05 0.12 0.02 0.39 0.26 0.03 0.00 0.12 0.05 0.15 0.03 0.58 0.18 OLFML2B 0.01 0.00 0.25 0.07 0.07 0.02 0.49 0.17 0.00 0.00 0.13 0.04 0.07 0.01 0.41 0.18 VAV3 0.03 0.00 0.34 0.02 0.04 0.02 0.51 0.16 0.01 0.00 0.05 0.03 0.06 0.00 0.39 0.11 GRIN2B 0.01 0.01 0.09 0.05 0.10 0.02 0.49 0.20 0.01 0.00 0.14 0.03 0.10 0.01 0.34 0.11 FAM171A1 0.00 0.00 0.27 0.08 0.06 0.01 0.33 0.12 0.01 0.00 0.01 0.06 0.21 0.00 0.21 0.08 CNTN4 0.03 0.00 0.01 0.07 0.07 0.00 0.38 0.09 0.00 0.00 0.19 0.05 0.05 0.02 0.21 0.10 ZNF804B 0.00 0.00 0.04 0.03 0.04 0.00 0.31 0.06 0.00 0.00 0.03 0.01 0.03 0.00 0.49 0.19 ZNF175 0.00 0.00 0.03 0.03 0.03 0.00 0.29 0.13 0.00 0.00 0.08 0.03 0.02 0.00 0.26 0.08 PTPRD 0.01 0.00 0.05 0.03 0.04 0.01 0.36 0.07 0.00 0.00 0.04 0.01 0.04 0.00 0.25 0.06 PIK3R4 0.01 0.00 0.05 0.01 0.02 0.00 0.41 0.20 0.00 0.00 0.03 0.03 0.01 0.00 0.11 0.09 PCDHB5 0.01 0.00 0.06 0.06 0.02 0.00 0.26 0.09 0.01 0.00 0.04 0.01 0.01 0.01 0.22 0.07 GALNT12 0.00 0.00 0.06 0.02 0.05 0.00 0.20 0.08 0.00 0.00 0.03 0.02 0.02 0.00 0.34 0.04 NRG3 0.00 0.00 0.09 0.00 0.01 0.00 0.14 0.41 0.00 0.00 0.00 0.01 0.01 0.00 0.09 0.03 ATP2C1 0.01 0.00 0.08 0.03 0.04 0.00 0.15 0.07 0.00 0.00 0.08 0.01 0.02 0.00 0.19 0.05
63 4.2 Targeted Sequencing of RLS Candidate Genes continued table…
Gene
Prevalence = 5% Prevalence = 10%
75% causal 100% causal 75% causal 100% causal
α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 DCLK2 0.00 0.00 0.10 0.03 0.03 0.00 0.23 0.05 0.00 0.00 0.14 0.02 0.02 0.00 0.06 0.07 SKOR1 0.00 0.00 0.06 0.03 0.03 0.00 0.21 0.07 0.00 0.00 0.06 0.01 0.01 0.00 0.19 0.05 DMPK 0.00 0.00 0.01 0.00 0.02 0.00 0.13 0.09 0.00 0.00 0.04 0.02 0.07 0.00 0.27 0.03 SLC14A2 0.00 0.00 0.04 0.02 0.02 0.00 0.20 0.05 0.00 0.00 0.07 0.02 0.00 0.00 0.15 0.10 LEO1 0.01 0.00 0.07 0.02 0.01 0.00 0.13 0.06 0.00 0.00 0.04 0.01 0.01 0.00 0.16 0.04 FAM114A1 0.00 0.00 0.03 0.02 0.01 0.00 0.13 0.05 0.00 0.00 0.09 0.00 0.01 0.00 0.15 0.03 CCDC148 0.00 0.00 0.09 0.01 0.00 0.00 0.15 0.02 0.00 0.00 0.07 0.01 0.00 0.00 0.09 0.04 SUN1 0.00 0.00 0.05 0.01 0.00 0.00 0.17 0.05 0.00 0.00 0.06 0.01 0.01 0.00 0.09 0.03 MAP2K5 0.00 0.00 0.14 0.00 0.00 0.00 0.04 0.05 0.00 0.00 0.08 0.00 0.01 0.00 0.13 0.03 ALLC 0.00 0.00 0.04 0.00 0.01 0.00 0.26 0.04 0.00 0.00 0.01 0.01 0.01 0.00 0.02 0.03 RASGRP4 0.00 0.00 0.03 0.02 0.01 0.00 0.11 0.04 0.00 0.00 0.04 0.01 0.01 0.00 0.10 0.04 PIAS1 0.00 0.00 0.01 0.00 0.01 0.00 0.12 0.03 0.00 0.00 0.06 0.03 0.00 0.00 0.10 0.03 PDE11A 0.00 0.00 0.08 0.01 0.01 0.00 0.09 0.06 0.00 0.00 0.02 0.01 0.00 0.00 0.07 0.02 EBF3 0.00 0.00 0.01 0.02 0.00 0.00 0.10 0.03 0.00 0.00 0.02 0.01 0.00 0.00 0.07 0.02 BBS7 0.00 0.00 0.03 0.01 0.00 0.00 0.08 0.03 0.00 0.00 0.01 0.01 0.00 0.00 0.07 0.02 SEMA6D 0.00 0.00 0.01 0.01 0.00 0.00 0.11 0.02 0.00 0.00 0.00 0.01 0.00 0.00 0.07 0.02 NTNG1 0.00 0.00 0.01 0.00 0.03 0.00 0.07 0.01 0.00 0.00 0.03 0.01 0.01 0.00 0.03 0.02 PKP4 0.00 0.00 0.03 0.01 0.00 0.00 0.07 0.02 0.00 0.00 0.02 0.01 0.00 0.00 0.04 0.01 ARFRP1 0.00 0.00 0.04 0.00 0.00 0.00 0.05 0.01 0.00 0.00 0.03 0.01 0.00 0.00 0.04 0.01 CACNG8 0.00 0.00 0.02 0.01 0.00 0.00 0.07 0.02 0.00 0.00 0.01 0.02 0.00 0.00 0.02 0.01 NECAP1 0.00 0.00 0.06 0.00 0.00 0.00 0.09 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.02 UNCX 0.00 0.00 0.02 0.01 0.00 0.00 0.04 0.02 0.00 0.00 0.01 0.01 0.00 0.00 0.04 0.02 KCNK13 0.00 0.00 0.06 0.00 0.00 0.00 0.04 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.04 0.01 SLC39A11 0.00 0.00 0.01 0.01 0.00 0.00 0.06 0.01 0.00 0.00 0.01 0.01 0.00 0.00 0.04 0.01 CREB5 0.00 0.00 0.01 0.00 0.00 0.00 0.08 0.02 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.02 SYT5 0.00 0.00 0.02 0.00 0.00 0.00 0.04 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.04 0.01 SGCZ 0.00 0.00 0.00 0.00 0.00 0.00 0.03 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.07 0.01 BTBD9 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.00 OSBP 0.00 0.00 0.01 0.00 0.00 0.00 0.06 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.01
64 4 Results continued table…
Gene
Prevalence = 5% Prevalence = 10%
75% causal 100% causal 75% causal 100% causal
α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 MEIS1 0.00 0.00 0.02 0.01 0.00 0.00 0.04 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.02 0.01 NPBWR2 0.00 0.00 0.01 0.01 0.00 0.00 0.03 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.03 0.01 CRBN 0.00 0.00 0.01 0.00 0.00 0.00 0.03 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.03 0.01 AAGAB 0.00 0.00 0.01 0.00 0.00 0.00 0.06 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.01 KCNA4 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.00 0.00 0.04 0.01 0.00 0.00 0.01 0.01 MICALL2 0.00 0.00 0.01 0.01 0.00 0.00 0.02 0.01 0.00 0.00 0.01 0.01 0.00 0.01 0.01 0.01 TUBB3 0.00 0.00 0.01 0.00 0.00 0.00 0.02 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.00 MPPED2 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.01 STEAP4 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.01 0.00 NRSN2 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 C7orf62 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.00 COLEC11 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 TREM1 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 MEIS2 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 FTSJ2 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CALML4 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 UBL4B 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 C15orf61 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 OSGIN1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 NENF 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 LRRN1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 CADM1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 OPRL1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 GLO1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 KRTAP19-5 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
65 4.2 Targeted Sequencing of RLS Candidate Genes Table 23: Power analysis for gene-level tests of 82 genes and sample size 10,000 : The median power is shown from 100 replicates (of gene models). CASC16 and LAMA1 were not included in the power analysis. The genes were ordered according to power over all scenarios. Green = genes with median power ≥ 0.8, OR = upper bound for OR of detrimental variants, causal = proportion of RLS causing variants in detrimental variants, α = type I error rate (for 100 and 20,000 independent null hypotheses, respectively).
Gene
Prevalence = 5% Prevalence = 10%
75% causal 100% causal 75% causal 100% causal
α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 TANC1 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 SETBP1 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 1.00 1.00 1.00 1.00 1.00 1.00 COL6A6 1.00 0.92 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.96 1.00 1.00 1.00 1.00 1.00 1.00 PTPRM 1.00 0.91 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.96 1.00 1.00 1.00 1.00 1.00 1.00 MYT1 1.00 0.86 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.96 1.00 0.99 1.00 1.00 1.00 1.00 COL20A1 0.99 0.81 1.00 0.99 1.00 1.00 1.00 1.00 0.95 0.82 1.00 0.99 1.00 1.00 1.00 1.00 ADAM22 1.00 0.87 1.00 0.96 1.00 0.99 1.00 1.00 1.00 0.93 0.87 0.92 1.00 0.99 1.00 1.00 MDGA1 1.00 0.81 1.00 1.00 1.00 0.99 1.00 1.00 1.00 0.42 0.99 0.98 1.00 0.97 1.00 1.00 EYA2 1.00 1.00 1.00 0.98 1.00 1.00 1.00 1.00 1.00 0.26 0.99 0.91 1.00 1.00 1.00 1.00 TOX3 1.00 0.97 1.00 0.95 1.00 1.00 1.00 1.00 0.90 0.84 1.00 0.44 1.00 0.99 1.00 1.00 ASTN2 1.00 0.90 1.00 0.46 1.00 1.00 1.00 1.00 0.93 0.70 1.00 0.99 1.00 1.00 1.00 1.00 IQCH 1.00 0.52 1.00 0.98 1.00 1.00 1.00 1.00 0.97 0.61 0.98 0.78 1.00 0.96 1.00 1.00 PLXNA2 1.00 0.32 1.00 0.98 1.00 1.00 1.00 1.00 0.98 0.46 1.00 1.00 1.00 1.00 1.00 1.00 GRIN2B 0.84 0.63 1.00 0.94 1.00 0.95 1.00 1.00 0.99 0.23 0.99 0.96 1.00 0.88 1.00 0.99 OLFML2B 0.35 0.74 1.00 0.99 1.00 0.99 1.00 1.00 0.96 0.70 0.86 0.86 1.00 0.75 1.00 1.00 VAV3 0.99 0.74 1.00 0.64 1.00 0.85 1.00 1.00 0.96 0.34 1.00 0.71 1.00 0.88 1.00 1.00 RIMS2 0.89 0.29 1.00 0.99 1.00 0.99 1.00 1.00 0.45 0.13 1.00 0.99 1.00 0.98 1.00 1.00 DCLK2 0.54 0.32 0.90 0.86 1.00 0.80 1.00 0.97 0.68 0.05 1.00 0.85 0.99 0.72 1.00 0.97 PCDHB5 0.61 0.17 1.00 0.94 0.98 0.80 1.00 1.00 0.99 0.01 1.00 0.37 0.99 0.75 1.00 0.97 GALNT12 0.54 0.03 0.99 0.48 0.99 0.77 1.00 0.96 0.94 0.29 0.99 0.58 1.00 0.76 1.00 0.94 ZNF175 0.47 0.43 0.99 0.86 0.92 0.78 1.00 0.99 0.83 0.43 0.84 0.06 0.91 0.36 1.00 0.97 CORO6 0.00 0.39 1.00 0.85 1.00 0.99 1.00 1.00 0.00 0.11 0.85 1.00 1.00 0.66 1.00 0.94 ATP2C1 0.59 0.18 0.98 0.64 0.99 0.77 1.00 0.98 0.63 0.22 0.89 0.58 0.91 0.56 1.00 0.88 PTPRD 0.63 0.16 0.99 0.27 1.00 0.74 1.00 0.90 0.66 0.13 0.86 0.70 0.99 0.78 1.00 0.94 SLC14A2 0.39 0.19 0.98 0.45 0.98 0.47 1.00 0.94 0.65 0.28 0.98 0.61 0.95 0.93 1.00 0.87 ZNF804B 0.75 0.54 0.99 0.17 1.00 0.63 1.00 0.87 0.50 0.08 0.75 0.70 1.00 0.70 1.00 0.92 DMPK 0.26 0.02 0.91 0.73 1.00 0.76 1.00 0.98 0.81 0.16 0.93 0.36 0.67 0.76 1.00 0.96 FAM171A1 0.99 0.57 0.78 0.12 1.00 0.72 1.00 0.99 0.03 0.29 1.00 0.07 1.00 0.68 1.00 0.96
66 4 Results continued table…
Gene
Prevalence = 5% Prevalence = 10%
75% causal 100% causal 75% causal 100% causal
α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 PIK3R4 0.99 0.07 0.94 0.65 1.00 0.70 1.00 0.87 0.47 0.05 0.83 0.34 0.75 0.41 1.00 0.95 LEO1 0.56 0.04 0.99 0.53 0.97 0.64 1.00 0.85 0.44 0.10 0.84 0.57 0.95 0.53 1.00 0.89 SKOR1 0.53 0.01 0.99 0.71 0.99 0.51 1.00 0.96 0.14 0.09 0.95 0.68 0.75 0.54 0.99 0.90 CNTN4 0.22 0.04 0.67 0.95 1.00 0.89 1.00 0.99 0.04 0.00 0.24 0.09 1.00 0.84 1.00 0.97 SUN1 0.46 0.27 0.98 0.67 0.95 0.30 0.99 0.83 0.30 0.13 0.85 0.16 0.71 0.40 0.99 0.76 FAM114A1 0.05 0.26 0.97 0.48 0.95 0.34 1.00 0.88 0.63 0.13 0.95 0.03 0.84 0.44 1.00 0.81 CCDC148 0.85 0.02 0.95 0.72 0.99 0.20 1.00 0.80 0.01 0.00 0.72 0.52 0.89 0.18 0.68 0.76 RASGRP4 0.31 0.07 0.83 0.43 0.91 0.30 0.98 0.80 0.47 0.10 0.58 0.42 0.77 0.36 0.97 0.75 NRG3 0.72 0.12 0.95 0.02 0.88 0.30 1.00 0.80 0.06 0.12 0.97 0.05 0.79 0.23 1.00 0.82 SEMA6D 0.53 0.01 0.92 0.47 0.86 0.18 0.98 0.96 0.01 0.00 0.74 0.29 0.34 0.13 0.94 0.84 PDE11A 0.41 0.03 0.82 0.19 0.82 0.31 0.97 0.61 0.04 0.00 0.60 0.26 0.69 0.59 0.92 0.53 ALLC 0.00 0.05 0.34 0.44 0.84 0.30 0.98 0.74 0.04 0.05 0.71 0.25 0.81 0.65 0.99 0.47 EBF3 0.24 0.03 0.65 0.39 0.73 0.35 0.98 0.59 0.14 0.04 0.66 0.10 0.71 0.20 0.91 0.83 PKP4 0.11 0.05 0.60 0.76 0.56 0.95 0.94 0.56 0.12 0.03 0.50 0.19 0.48 0.14 1.00 0.44 BBS7 0.23 0.05 0.48 0.25 0.71 0.19 0.98 0.73 0.27 0.03 0.68 0.25 0.68 0.12 0.95 0.72 MAP2K5 0.04 0.00 0.02 0.52 0.96 0.57 1.00 1.00 0.00 0.00 0.01 0.01 0.86 0.30 1.00 0.87 NECAP1 0.22 0.05 0.97 0.03 0.46 0.50 0.92 0.65 0.12 0.04 0.06 0.57 0.63 0.15 1.00 0.60 PIAS1 0.00 0.07 0.97 0.02 0.87 0.22 0.97 0.80 0.00 0.13 0.13 0.02 0.73 0.24 0.98 0.71 MICALL2 0.04 0.01 0.56 0.01 0.33 0.90 0.82 0.17 0.02 0.01 0.33 0.04 1.00 0.92 0.60 0.98 CACNG8 0.00 0.11 0.49 0.07 0.65 0.02 0.94 0.62 0.00 0.08 0.87 0.03 0.67 0.15 0.90 0.55 CREB5 0.01 0.06 0.25 0.43 0.79 0.06 0.96 0.70 0.31 0.05 0.07 0.04 0.48 0.18 0.94 0.58 KCNK13 0.00 0.07 0.81 0.03 0.86 0.09 0.84 0.82 0.31 0.03 0.37 0.03 0.40 0.05 0.83 0.34 UNCX 0.13 0.04 0.51 0.28 0.56 0.14 0.89 0.50 0.11 0.01 0.42 0.13 0.28 0.07 0.86 0.43 SLC39A11 0.21 0.02 0.53 0.09 0.53 0.10 0.84 0.46 0.09 0.01 0.44 0.25 0.38 0.05 0.84 0.37 NTNG1 0.29 0.00 0.24 0.16 0.67 0.12 0.97 0.43 0.05 0.01 0.12 0.11 0.55 0.02 0.76 0.43 ARFRP1 0.00 0.00 0.87 0.08 0.48 0.00 0.88 0.45 0.34 0.00 0.00 0.00 0.37 0.06 0.82 0.35 SYT5 0.12 0.00 0.63 0.16 0.33 0.11 0.69 0.43 0.09 0.01 0.26 0.09 0.23 0.06 0.73 0.42 SGCZ 0.01 0.00 0.75 0.01 0.76 0.06 0.81 0.36 0.00 0.01 0.03 0.00 0.32 0.03 0.74 0.14 NPBWR2 0.01 0.01 0.51 0.12 0.30 0.05 0.68 0.27 0.03 0.02 0.40 0.01 0.29 0.03 0.64 0.36
67 4.2 Targeted Sequencing of RLS Candidate Genes continued table…
Gene
Prevalence = 5% Prevalence = 10%
75% causal 100% causal 75% causal 100% causal
α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 α = 2.5E-06 α = 5E-04 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OR = 4 OR = 3 OSBP 0.05 0.05 0.26 0.18 0.36 0.03 0.38 0.65 0.21 0.00 0.01 0.16 0.31 0.00 0.68 0.22 CRBN 0.04 0.00 0.33 0.04 0.26 0.04 0.76 0.27 0.04 0.01 0.11 0.04 0.21 0.02 0.52 0.25 MEIS1 0.03 0.00 0.16 0.03 0.22 0.04 0.68 0.22 0.04 0.00 0.35 0.11 0.06 0.02 0.63 0.25 MPPED2 0.04 0.01 0.57 0.07 0.10 0.01 0.69 0.26 0.00 0.00 0.04 0.02 0.06 0.01 0.58 0.17 KCNA4 0.03 0.00 0.07 0.38 0.08 0.01 0.44 0.11 0.27 0.00 0.67 0.03 0.04 0.01 0.14 0.03 TUBB3 0.01 0.00 0.14 0.11 0.11 0.02 0.44 0.18 0.01 0.00 0.11 0.16 0.07 0.03 0.39 0.13 AAGAB 0.02 0.00 0.55 0.02 0.12 0.02 0.36 0.11 0.00 0.00 0.08 0.01 0.06 0.01 0.33 0.17 STEAP4 0.02 0.00 0.20 0.05 0.06 0.01 0.45 0.15 0.02 0.00 0.09 0.06 0.04 0.01 0.34 0.14 MEIS2 0.00 0.00 0.01 0.01 0.00 0.00 0.03 0.01 0.00 0.00 0.51 0.00 0.00 0.10 0.87 0.01 BTBD9 0.75 0.00 0.06 0.01 0.03 0.00 0.25 0.07 0.00 0.00 0.03 0.01 0.02 0.00 0.21 0.06 FTSJ2 0.00 0.02 0.05 0.01 0.00 0.10 0.03 0.03 0.14 0.00 0.00 0.00 0.00 0.00 0.95 0.01 NRSN2 0.01 0.00 0.05 0.01 0.03 0.00 0.22 0.05 0.01 0.00 0.04 0.04 0.01 0.00 0.19 0.06 COLEC11 0.00 0.00 0.09 0.02 0.02 0.00 0.19 0.07 0.00 0.00 0.03 0.01 0.01 0.00 0.18 0.06 OPRL1 0.04 0.00 0.00 0.00 0.00 0.00 0.64 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 TREM1 0.01 0.00 0.08 0.03 0.01 0.00 0.16 0.06 0.00 0.00 0.02 0.01 0.01 0.00 0.15 0.05 C7orf62 0.01 0.00 0.00 0.00 0.00 0.00 0.02 0.01 0.00 0.00 0.28 0.00 0.00 0.00 0.03 0.23 CALML4 0.00 0.00 0.01 0.00 0.00 0.00 0.06 0.01 0.00 0.00 0.00 0.01 0.00 0.00 0.34 0.01 C15orf61 0.00 0.00 0.01 0.01 0.00 0.00 0.05 0.02 0.00 0.00 0.03 0.00 0.00 0.00 0.05 0.01 UBL4B 0.00 0.00 0.01 0.01 0.00 0.00 0.05 0.02 0.00 0.00 0.02 0.01 0.00 0.00 0.03 0.01 OSGIN1 0.03 0.00 0.03 0.00 0.00 0.00 0.04 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.03 0.01 LRRN1 0.00 0.00 0.01 0.00 0.00 0.00 0.02 0.01 0.00 0.00 0.00 0.01 0.00 0.00 0.04 0.00 NENF 0.00 0.00 0.01 0.01 0.00 0.00 0.03 0.01 0.00 0.00 0.01 0.00 0.00 0.00 0.02 0.01 GLO1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.04 CADM1 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01 0.00 KRTAP19-5 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
4 Results
4.2.4.3 Analysis of MIPseq Data from the Case-Control Cohort