Table 2 Analytical validation for standard WES and extended WES

From: Augmenting cost-effectiveness in clinical diagnosis using extended whole-exome sequencing: SNVs, SVs, and beyond

Sequencing methods and samples

Benchmark region size (bp)

# High confidence SNVs and indels

Recall

Precision

F1 score

J-insurance CDS for standard WES of HG001

535,105

297

0.980

0.997

0.988

J-insurance CDS for standard WES of HG002

555,044

317

0.981

0.997

0.989

J-insurance CDS for extended WES of HG001

535,105

297

0.980

0.993

0.986

J-insurance CDS for extended WES of HG002

555,044

317

0.984

0.997

0.990

J-insurance CDS for extended WGS of HG001

535,105

297

0.966

0.997

0.981

J-insurance CDS for extended WGS of HG002

555,044

317

0.994

1.000

0.997

J-insurance intronic+UTRs for standard WES of HG001

7,562,731

8900

0.242

0.864

0.378

J-insurance intronic+UTRs for standard WES of HG002

7,626,118

9313

0.224

0.857

0.355

J-insurance intronic+UTRs for extended WES of HG001

7,562,731

8900

0.909

0.925

0.917

J-insurance intronic+UTRs for extended WES of HG002

7,626,118

9313

0.905

0.921

0.913

J-insurance intronic+UTRs for extended WGS of HG001

7,562,731

8 900

0.983

0.991

0.987

J-insurance intronic+UTRs for extended WGS of HG002

7,626,118

9 313

0.990

0.991

0.990

ACMG SF genes CDS for standard WES of HG001

326,938

161

0.994

1.000

0.997

ACMG SF genes CDS for standard WES of HG002

345,845

162

1.000

0.988

0.994

ACMG SF genes CDS for extended WES of HG001

326,938

161

0.994

1.000

0.997

ACMG SF genes CDS for extended WES of HG002

345,845

162

1.000

1.000

1.000

ACMG SF genes CDS for extended WGS of HG001

326,938

161

0.975

0.994

0.984

ACMG SF genes CDS for extended WGS of HG002

345,845

162

1.000

1.000

1.000

ACMG SF genes intronic+UTRs for standard WES of HG001

5,397,183

7399

0.185

0.841

0.303

ACMG SF genes intronic+UTRs for standard WES of HG002

5,447,687

7906

0.158

0.851

0.267

ACMG SF genes intronic+UTRs for extended WES of HG001

5,397,183

7399

0.910

0.936

0.923

ACMG SF genes intronic+UTRs for extended WES of HG002

5,447,687

7906

0.912

0.921

0.916

ACMG SF genes intronic+UTRs for extended WGS of HG001

5,397,183

7399

0.988

0.991

0.989

ACMG SF genes intronic+UTRs for extended WGS of HG002

5,447,687

7906

0.991

0.991

0.991

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