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Table 2 Detection probability for causal genes.

From: A 2-step penalized regression method for family-based next-generation sequencing association studies

 

DBP at exam 1

SBP at exam 1

Gene

All variants

<5% MAF variants

All variants

<5% MAF variants

 

0.5

0.9

0.5

0.9

0.5

0.9

0.5

0.9

ABTB1

0.005

0.005

0

0

0

0.005

0

0

ARF4

0.005

0.005

0.025

0.025

0.020

0.020

0.035

0.035

ARHGEF3

0.025

0.125

0.110

0.185

0.030

0.130

0.100

0.155

B4GALT4

0

0

0.010

0.030

0

0

0

0

BTD

0.005

0.030

0.020

0.025

0

0.025

0.010

0.015

CXCR6

0

0

0

0

0

0

0

0

DNASE1L3

0.005

0.010

0.020

0.035

0.005

0.010

0.025

0.055

FBLN2

0.005

0.080

0.075

0.120

0.010

0.085

0.060

0.125

FLNB

0.035

0.110

0.095

0.130

0.120

0.360

0.100

0.140

GPR160

0

0.015

0

0.005

0

0.005

0

0

LOC152217

0

0

0

0

0

0.000

0

0

MAP4

0.995

1.000

1.000

1.000

0.990

0.995

1.000

1.000

MLH1

0.010

0.015

0.020

0.030

0

0

0

0.005

MUC13

0.005

0.015

0.065

0.120

0.005

0.020

0.045

0.100

NMNAT3

0.015

0.040

0.010

0.040

0.015

0.045

0.015

0.045

PAK2

0.005

0.045

0.030

0.055

0.010

0.035

0.030

0.060

PDCD6IP

0.010

0.015

0.015

0.020

0.010

0.020

0.015

0.015

PPP2R3A

0.005

0.005

0.035

0.045

0.010

0.015

0.025

0.025

PROK2

0.005

0.005

0.010

0.015

0

0

0.005

0.005

PTPLB

0.005

0.015

0.050

0.080

0.005

0.010

0.030

0.045

RAD18

0

0.035

0

0.005

0

0.020

0.005

0.005

RYBP

0.015

0.025

0.025

0.040

0.005

0.005

0.020

0.035

SCAP

0.180

0.185

0.260

0.260

0.150

0.155

0.210

0.210

SEMA3F

0.005

0.005

0.015

0.020

0

0

0

0

SENP5

0

0.010

0.030

0.075

0.005

0.015

0.010

0.020

SERP1

0

0

0

0.000

0

0.005

0.000

0

SUMF1

0

0.035

0.065

0.120

0

0.050

0.115

0.190

TFDP2

0.005

0.010

0.040

0.065

0

0

0.030

0.040

TUSC2

0

0

0

0

0

0

0

0

VPS8

0.005

0.030

0.050

0.095

0.015

0.020

0.090

0.130

ZBTB38

0.015

0.090

0.085

0.140

0.005

0.070

0.080

0.200

  1. The proportion of the 200 simulation replicates that each causal gene (contains at least 1 variant with a DBP or SBP effect) is present in the selected in the final penalized regression model.
  2. Each examined model specifies 134 predictors to be selected with nonzero regression coefficients using either a 50% or 90% weighting between the pure lasso and group penalties (ie, λ L λ L + λ E =0.5 or 0.9) and with either all variants or only those with MAF less than 5%.