Table 1 Summary of genome-wide structural variants associated with hematological trait

From: Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program

 

TOPMed Allele Frequencies

Significant single variant association tests

Gene(s)

Locus

SV Breakpoints¹

SV type²

Length (bp)

Overall

African³

Asian³

Hispanic³

European³

Significant Trait

Effect Estimate

SE

P-value

-

2p11.24

2:88832769-88860930

DEL

28162

1.98E-04

4.06E-05

0

0

2.98E-04

Lymphocytes

1.878

0.310

1.36E-09

WBC

2.813

0.426

3.84E-11

RAB7A

3q21.3

3:128694260-128695207

DUP

948

0.085

0.022

0.031

0.065

0.119

Monocyte prop.

−0.002

0.0004

6.91E-09

SRPRB, TF, TOPBP1

3q22.1

3:133621201-133784900

DUP

163700

0.208

0.141

0.308

0.200

0.236

TIBC

20.809

2.209

4.56E-21

UIBC

19.298

2.553

4.09E-14

C3orf36, LINC02000, RAB6B, SLCO2A1, SRPRB, TF

3q22.1-q22.2

3:133786201-134102300

DUP

316100

0.272

0.207

0.358

0.267

0.292

TIBC

17.804

2.324

1.84E-14

UIBC

19.463

2.687

4.35E-13

PSORS1C1

6p21.33

6:31132409-31132465

DEL

57

0.085

0.049

0.075

0.103

0.094

Lymphocytes

0.075

0.012

2.01E-09

-

6p21.32

6:32591559-32591660

DEL

102

0.264

0.167

0.281

0.293

0.293

WBC

0.092

0.015

1.25E-09

-

6p21.1

6:41897089-41897626

DEL

538

0.183

0.079

0.209

0.151

0.235

MCH

−0.187

0.022

1.28E-17

MCV

−0.595

0.055

3.04E-27

RBC

0.033

0.005

1.57E-12

CCND3

6p21.1

6:41985574-41988887

DEL

3314

0.007

0.002

0.001

0.007

0.010

MCV

1.556

0.256

1.16E-09

-

6p23.3

6:134878573-134878641

DUP

69

0.044

0.072

0.030

0.037

0.036

MCH

−0.254

0.046

4.23E-08

-

9q22.1

9:88923551-88924152

DEL

602

0.034

0.117

7.08E-04

0.032

7.31E-04

Monocytes

−0.029

0.004

2.20E-11

Monocyte prop.

−0.004

−0.004

1.07E-12

ATXN2

12q24.12

12:111538485-111542205

DEL

3721

0.068

0.016

0.021

0.058

0.092

Platelets

−6.063

0.820

1.40E-13

ATXN2

12q24.12

12:111542097-111542205

INV

109

0.062

0.015

0.021

0.054

0.085

Platelets

−6.371

0.911

2.65E-12

-

14q32.334

14:105863184-105897962

DEL

34779

2.24E-04

4.16E-05

0

0

3.43E-04

Lymphocytes

2.037

0.256

1.87E-15

Lymphocyte prop.

0.228

0.030

2.49E-14

Neutrophil prop.

−0.222

0.034

1.08E-10

-

14q32.334

14:105864247-105902650

DEL

38404

7.96E-05

0

0

0

1.41E-04

WBC

3.115

0.483

1.15E-10

HBA1, HBA2

16p13.3

16:165396-184701

DEL

19306

5.95E-05

0

0.004

6.32E-05

0

MCH

−6.570

0.865

3.12E-14

MCV

−16.599

2.305

5.97E-13

RBC

1.437

0.189

3.02E-14

HBA1, HBA2

16p13.3

16:172001-177200

DEL

5200

0.057

0.176

0.030

0.060

0.008

Hematocrit

−0.485

0.054

2.65E-19

Hemoglobin

−0.437

0.018

5.06E-127

MCH

−2.668

0.038

<5E-324

MCHC

−0.701

0.015

<5E-324

MCV

−6.276

0.099

<5E-324

RBC

0.296

0.008

<5E-324

RBW

0.545

0.030

1.19E-73

MPV

0.118

0.021

1.60E-08

FAM234A

16p13.3

16:246437-249971

DEL

3535

0.006

0.019

7.39E-04

0.005

7.54E-05

MCH

−0.788

0.120

4.90E-11

MCV

−1.917

0.310

6.07E-10

CAPN15

16p13.3

16:550075-550141

DEL

67

0.025

0.116

7.05E-04

0.020

3.39E-04

MCH

−0.374

0.063

2.92E-09

MCV

−0.929

0.162

8.74E-09

KCNJ18

17p11.2

17:21659501-21795800

DUP

136300

0.511

0.519

0.509

0.508

0.508

Lymphocyte prop.

0.022

0.004

4.36E-10

Neutrophils prop.

−0.025

0.004

3.90E-10

-

18p11.22

18:9621931-9622237

DEL

307

0.791

0.839

0.921

0.766

0.770

MPV

−0.079

0.014

9.32E-09

TMPRSS6

22q12.3

22:37067818-37067888

DUP

71

0.347

0.483

0.323

0.324

0.301

Hemoglobin

0.059

0.010

1.62E-08

  1. ¹Structural variant breakpoints predicted by the Parliament2 pipeline.
  2. ²Types of structural variant identified: deletions (DEL), duplications (DUP), inversions (INV).
  3. ³Discrete ancestry subgroups are based on genetically inferred ancestry and a machine learning algorithm that refines self-identified ancestry.
  4. 4Based on location and WGS read visualization SV likely represents a somatic deletion or a complex rearrangement due to V(D)J recombination events.
  5. All p-values are derived from two-sided t-tests and are not adjusted for multiple comparisons. WBC White Blood Cells, TIBC Total iron binding capacity, UIBC Unsaturated iron binding capacity, MCH Mean corpuscular hemoglobin, MCV Mean corpuscular volume, RBC Red blood cells, RBW Red cell width, MCHC Mean corpuscular hemoglobin concentration, MPV Mean Platelet Volume.
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