Risteys · CD2_BENIGN

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions None	520210
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D30 Cause of death: ICD-10 — D30 2 out of 7 registries used, show all original rules.	1501
4. Check minimum number of events None	1501
5. Include endpoints CD2_BENIGN_KIDNEY CD2_BENIGN_RENALPELVIS CD2_BENIGN_URETER CD2_BENIGN_BLADDER CD2_BENIGN_URETHRA CD2_BENIGN_URINARY_NOS	1668
6. Filter based on genotype QC (FinnGen only)	1668

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	10630	5830	4676
Only index persons	8788	5122	3666
Unadjusted period prevalence (%)
Whole population	0.15	0.17	0.13
Only index persons	0.17	0.19	0.14
Median age at first event (years)
Whole population	62.94	61.07	65.27
Only index persons	61.73	59.80	64.43

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	1668	931	737
Unadjusted period prevalence (%)	0.32	0.32	0.32
Median age at first event (years)	61.61	57.81	66.42

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

↥

CodeWAS is a tool for exploring the associations between an endpoint and all of the medical codes and drug codes.

This is a new tool, please reach out using the contact form for feedback and improvement ideas.

First, a cohort is built by matching controls to the endpoint cases using year of birth and sex. Then, a Fisher test is done for all the medical codes and drug codes between the cases and controls of this cohort. Codes are reported in the table below if they have −log₁₀(p-value) ≥ 6.

Matched cohort

Matched cases
1480: Matched controls
14794

Code

Vocabulary

Description

Odds Ratio

-log₁₀(p)

N matched cases

N matched controls

D30.0

ICD-10 Finland

Benign neoplasm: Kidney

16384.0

323.0

977

D41.0

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Kidney

43.7

323.0

452

147

D30.3

ICD-10 Finland

Benign neoplasm: Bladder

+∞

256.9

239

C64.88

ICD-10 Finland

Other malignant neoplasm of kidney, except renal pelvis

18.3

136.7

218

138

UKC02

NOMESCO Finland

Cystoscopy

4.4

118.2

528

1645

KAD00

NOMESCO Finland

Partial nephrectomy

61.3

88.3

103

KCD02

NOMESCO Finland

Transurethral resection of bladder

10.0

71.8

149

163

KAD01

NOMESCO Finland

Percutaneous endoscopic partial nephrectomy

54.7

61.5

KA1AE

NOMESCO Finland

Kidney ultrasound examination

9.3

61.0

131

152

R31

ICD-10 Finland

Unspecified haematuria

3.5

50.7

274

913

KAC10

NOMESCO Finland

Total nephrectomy with capsule

16.4

49.7

KA3AT

NOMESCO Finland

Biopsy of kidney with ultrasound guidance

13.2

47.6

D30.1

ICD-10 Finland

Benign neoplasm: Renal pelvis

+∞

46.1

D30.9

ICD-10 Finland

Benign neoplasm: Urinary organ, unspecified

+∞

46.1

D30.4

ICD-10 Finland

Benign neoplasm: Urethra

+∞

42.9

KAC11

NOMESCO Finland

Total nephrectomy with capsule, transcutaneous

23.6

41.2

2230A

ICD-9 Finland

Benign neoplasm of kidney and other urinary organs, Kidney, except pelvis

+∞

39.8

D41.4

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Bladder

7.6

39.0

131

C67.8

ICD-10 Finland

Malignant neoplasm: Overlapping lesion of bladder

7.3

36.9

131

2233A

ICD-9 Finland

Benign neoplasm of kidney and other urinary organs, Bladder

+∞

36.6

WX408

NOMESCO Finland

General anesthesy, balanced

2.2

35.7

476

2634

PC5DT

NOMESCO Finland

Embolisation of tumor of kidney

+∞

31.4

R10.4

ICD-10 Finland

Other and unspecified abdominal pain

2.0

31.3

559

3449

KCD32

NOMESCO Finland

Cystoscopic destruction of tumour of bladder

13.2

31.3

8312/3-C64.9

ICD-O-3

Renal cell carcinoma, NOS, of kidney, NOS

10.7

30.8

KH1AE

NOMESCO Finland

Urinary tract ultrasound examination

3.6

29.7

144

434

JN3AE

NOMESCO Finland

Abdominal ultrasound examination

2.5

29.2

262

1180

JN3CD

NOMESCO Finland

Abdominal CT examination both without and with contrast

4.3

29.0

111

271

N28.1

ICD-10 Finland

Cyst of kidney

8.4

28.7

N02BE01

ATC

paracetamol; systemic, rectal

2.3

28.6

1285

11000

WX302

NOMESCO Finland

Thoracal epidural anesthesy

3.7

28.4

130

373

C67.9

ICD-10 Finland

Malignant neoplasm: Bladder, unspecified

7.3

27.6

22330

ICD-8 Finland

Benign neoplasm of kidney and other urinary organs, Bladder

+∞

27.2

N02AX02

ATC

tramadol; systemic, rectal

1.8

25.3

680

4741

JN1CD

NOMESCO Finland

Very extensive CT examination of upper part of abdomen

10.5

24.6

8120/3-C67.9

ICD-O-3

Transitional cell carcinoma, NOS, of bladder, NOS

6.3

23.6

106

JN3BD

NOMESCO Finland

Extensive abdominal CT

2.4

23.0

208

931

JN3AD

NOMESCO Finland

Abdominal CT examination

2.8

22.8

156

594

KH1CD

NOMESCO Finland

Very extensive urinary tract ultrasound examination

7.4

22.6

22300

ICD-8 Finland

Benign neoplasm of kidney and other urinary organs, Kidney, except pelvis

+∞

20.9

J01MA02

ATC

ciprofloxacin; systemic

1.7

20.8

604

4233

C67.2

ICD-10 Finland

Malignant neoplasm: Lateral wall of bladder

7.8

20.4

7323

FHL

Electrosection of TU bladder wall change

27.4

20.1

UKC05

NOMESCO Finland

Cystoscopy and bladder biopsy

7.5

20.0

TPH07

NOMESCO Finland

Cathetrisation of artery

2.4

20.0

188

858

B01AB05

ATC

enoxaparin; parenteral

1.8

19.8

472

3102

WX404

NOMESCO Finland

Intravenous generell anesthesy

1.9

19.6

329

1918

KAC00

NOMESCO Finland

Nephrectomy

21.9

19.5

KCD05

NOMESCO Finland

Excision of bladder lesion during urinary tract endoscopy with photodynamic diagnosis (PDD)

8.3

19.5

J01DB01

ATC

cefalexin; oral

1.8

19.4

1164

9958

PC5ET

NOMESCO Finland

Extensive embolisation of tumor of kidney

+∞

18.8

D30.2

ICD-10 Finland

Benign neoplasm: Ureter

+∞

18.8

KH1BD

NOMESCO Finland

Extensive urinary tract CT examination

8.5

18.5

JN1BD

NOMESCO Finland

Extensive CT examination of upper part of abdomen

12.0

18.3

R93.4

ICD-10 Finland

Abnormal findings on diagnostic imaging of urinary organs

22.0

18.2

XKD00

NOMESCO Finland

Uroflowmetry

2.0

18.1

278

1565

22388

ICD-8 Finland

Benign neoplasm of kidney and other urinary organs, Other specified sites

+∞

17.7

N18.9

ICD-10 Finland

Chronic kidney disease, unspecified

2.7

17.6

126

493

1530

FHL

Urethrocystoscopy

4.5

17.4

142

8310/3-C64.9

ICD-O-3

Clear cell adenocarcinoma, NOS, of kidney, NOS

7.7

16.9

GD1AA

NOMESCO Finland

Thorax X-ray examination

1.6

16.6

661

4955

XF603

NOMESCO Finland

Direct intraarterial blood pressure measurement

3.4

16.5

242

I10

ICD-10 Finland

Essential (primary) hypertension

1.6

15.9

895

7275

8120/1-C67.9

ICD-O-3

Urothelial papilloma, NOS, of bladder, NOS

+∞

15.6

ZXD10

NOMESCO Finland

Scheduled procedure

1.6

15.4

576

4227

A02BC02

ATC

pantoprazole; systemic

1.6

15.1

942

7805

KC1EE

NOMESCO Finland

Ultrasound measurement of residual urine

2.0

15.1

223

1232

R10.1

ICD-10 Finland

Pain localized to upper abdomen

1.9

14.7

243

1398

A02BC05

ATC

esomeprazole; systemic

1.6

14.7

574

4241

KAC20

NOMESCO Finland

Nephroureterectomy

80.9

14.6

UJF32

NOMESCO Finland

Coloscopy

1.7

14.4

396

2666

G04CA02

ATC

tamsulosin; oral

1.7

14.1

357

2348

7321

FHL

TU biopsy, coagulation or laser

12.8

13.9

TPH04

NOMESCO Finland

Cathetrisation of vein

1.7

13.6

315

2015

JN4BD

NOMESCO Finland

Extensive body CT

2.0

13.6

191

1032

KBV02

NOMESCO Finland

Cystoscopic insertion of stent into ureter

4.0

13.5

135

WX320

NOMESCO Finland

Spinalanesthesy

1.7

13.4

340

2232

U14

ICPC

Kidney symptom/complaint

4.9

13.3

UJD10

NOMESCO Finland

Esophagoscopy, gastroscopy and duodenoscopy

1.6

13.2

437

3079

8260/3-C64.9

ICD-O-3

Papillary adenocarcinoma, NOS, of kidney, NOS

15.2

13.1

ZXE00

NOMESCO Finland

One hour or less

1.5

13.1

557

4167

N10

ICD-10 Finland

Acute tubulo-interstitial nephritis

1.9

13.0

201

1125

ZXE10

NOMESCO Finland

More than one and less than three hours

1.5

12.7

529

3927

KCW02

NOMESCO Finland

Lavation of bladder for coagulated blood

6.2

12.6

D41.9

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Urinary organ, unspecified

70.4

12.6

R10.3

ICD-10 Finland

Pain localized to other parts of lower abdomen

1.7

12.5

274

1722

WX602

NOMESCO Finland

Repeated or continuing anesthesia shots throug a catheter

2.2

12.2

126

599

UKB02

NOMESCO Finland

Retrograde ureteroscopy

5.8

12.0

K57.3

ICD-10 Finland

Diverticular disease of large intestine without perforation or abscess

1.7

12.0

283

1815

C64

ICD-10 Finland

Malignant neoplasm of kidney, except renal pelvis

7.1

11.8

WX110

NOMESCO Finland

Local anesthesy

1.5

11.5

894

7530

D30.7

ICD-10 Finland

Benign neoplasm: Other urinary organs

+∞

11.5

KH1AD

NOMESCO Finland

CT of urinary organs

3.1

11.3

197

J01EA01

ATC

trimethoprim; systemic

1.6

11.2

376

2638

C65

ICD-10 Finland

Malignant neoplasm of renal pelvis

14.0

11.0

ZXA00

NOMESCO Finland

Right side

1.5

10.9

402

2880

JN1CG

NOMESCO Finland

Extensive MRI examination of upper part of abdomen with high intensity magnet

3.4

10.9

152

R4110

NOMESCO Finland

Physiotherapy

1.6

10.8

375

2648

D41.1

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Renal pelvis

13.0

10.6

P01AB01

ATC

metronidazole; oral, rectal

1.5

10.6

528

4044

A02BC03

ATC

lansoprazole; oral

1.5

10.2

422

3097

JN4AD

NOMESCO Finland

Body CT examination

2.0

9.9

120

612

N02AJ06

ATC

codeine and paracetamol; systemic

1.5

9.8

466

3518

N20.1

ICD-10 Finland

Calculus of ureter

2.7

9.8

253

R50.9

ICD-10 Finland

Fever, unspecified

1.7

9.7

194

1178

WX402

NOMESCO Finland

General anaesthesia

1.7

9.7

210

1310

Z71.2

ICD-10 Finland

Person consulting for explanation of investigation findings

1.6

9.6

312

2162

K80.2

ICD-10 Finland

Calculus of gallbladder without cholecystitis

1.8

9.4

170

1001

U07

ICPC

Urine symptom/complaint other

2.2

9.4

446

8130/1-C67.9

ICD-O-3

Papillary urothelial neoplasm of low malignant potential of bladder, NOS

30.2

9.4

PC5SC

NOMESCO Finland

Selective angiography of kidney artery with X-ray

30.2

9.4

JN1AE

NOMESCO Finland

Ultrasound examination of upper part of abdomen

2.0

9.4

126

670

KCB00

NOMESCO Finland

Biopsy of bladder

8.7

9.3

EP1AE

NOMESCO Finland

Neck ultrasound examination

2.2

9.3

431

ZXE20

NOMESCO Finland

More than three and less than five hours

1.7

9.2

210

1324

R33

ICD-10 Finland

Retention of urine

1.9

9.2

128

687

7125

FHL

Nephrectomy (extrrafascial)

13.8

9.2

WX700

NOMESCO Finland

Respiratory and circulatory monitoring

1.6

9.0

223

1443

J01MA12

ATC

levofloxacin; systemic

1.6

9.0

272

1850

KBE12

NOMESCO Finland

Transluminal endoscopic extraction of calculus of ureter

5.1

9.0

S18

ICPC

Laceration/cut

1.4

8.9

587

4703

WX002

NOMESCO Finland

Sedation and analgesia

1.5

8.7

286

1981

Z2221

NOMESCO Finland

Medical doctor

1.5

8.7

372

2737

N39.0

ICD-10 Finland

Urinary tract infection, site not specified

1.6

8.5

208

1336

M01AE03

ATC

ketoprofen; systemic, rectal

1.4

8.5

530

4193

Z3231

NOMESCO Finland

Registered nurse

1.5

8.5

379

2807

WZC00

NOMESCO Finland

Planning of intervention or health care consultation

1.4

8.5

426

3232

KA3LT

NOMESCO Finland

Njurlesion coagulation

20.1

8.5

A06AC01

ATC

ispaghula (psylla seeds); oral

1.5

8.4

344

2503

18899

ICD-8 Finland

Malignant neoplasm of bladder

90.5

8.4

22399

ICD-8 Finland

Benign neoplasm of kidney and other urinary organs, Unspecified site

+∞

8.3

JN4CD

NOMESCO Finland

Very extensive body CT

2.3

8.3

315

C67.0

ICD-10 Finland

Malignant neoplasm: Trigone of bladder

9.5

8.3

ZXA05

NOMESCO Finland

Left side

1.5

8.1

372

2767

5997A

ICD-9 Finland

Other disorders of urethra and urinary tract, Haematuria

8.2

8.1

U79

ICPC

Neoplasm urinary tract unspecified

33.5

8.1

JN3KE

NOMESCO Finland

Abdominal ultrasound with added contrast

6.9

8.1

C67.4

ICD-10 Finland

Malignant neoplasm: Posterior wall of bladder

22.1

8.0

JKA21

NOMESCO Finland

Laparoscopic cholecystectomy

1.7

7.9

153

923

B01AB10

ATC

tinzaparin; parenteral

1.9

7.8

107

574

Z3226

NOMESCO Finland

Physiotherapist

1.5

7.7

252

1742

C08CA01

ATC

amlodipine; oral

1.4

7.7

514

4101

KAC01

NOMESCO Finland

Percutaneous endoscopic nephrectomy

18.4

7.6

D01

ICPC

Abdominal pain/cramps general

1.8

7.5

134

788

1888X

ICD-9 Finland

Malignant neoplasm of bladder, Other specified sites of bladder

13.4

7.4

C67.1

ICD-10 Finland

Malignant neoplasm: Dome of bladder

13.4

7.4

D02

ICPC

Abdominal pain epigastric

2.1

7.4

385

N03AX16

ATC

pregabalin; oral

1.5

7.4

309

2253

R35

ICD-10 Finland

Polyuria

2.0

7.3

500

R30.0

ICD-10 Finland

Dysuria

2.4

7.3

239

N18.8

ICD-10 Finland

Other chronic renal failure

2.7

7.2

178

M54.5

ICD-10 Finland

Low back pain

1.4

7.2

399

3069

KED22

NOMESCO Finland

Transurethral resection of prostate

2.0

7.2

491

N02AA59

ATC

codeine, combinations excl. psycholeptics; systemic

1.4

7.2

587

4826

Q85.1

ICD-10 Finland

Tuberous sclerosis

30.1

7.1

8317/3-C64.9

ICD-O-3

Renal cell carcinoma, chromophobe type of kidney, NOS

20.1

7.1

Z01.8

ICD-10 Finland

Other specified special examinations

1.5

7.1

281

2024

ZXD05

NOMESCO Finland

Urgent procedure

1.4

7.0

403

3116

N13.3

ICD-10 Finland

Other and unspecified hydronephrosis

2.9

7.0

139

N20.0

ICD-10 Finland

Calculus of kidney

3.0

6.9

125

G04CA01

ATC

alfuzosin; oral

1.6

6.9

160

1014

C64.80

ICD-10 Finland

Wilms tumour

13.8

6.9

J01MA06

ATC

norfloxacin; oral

1.6

6.9

187

1238

C07AB07

ATC

bisoprolol; oral

1.3

6.8

670

5654

GD1UA

NOMESCO Finland

Thorax X-ray examination outside radiological department

1.5

6.7

204

1386

KB1CG

NOMESCO Finland

Extensive MRI examination of urinary tract with high intensity magnet

22.6

6.7

XKD06

NOMESCO Finland

Physiologic investigation of micturition

2.5

6.6

195

T81.4

ICD-10 Finland

Infection following a procedure, not elsewhere classified

1.7

6.6

143

890

UJF45

NOMESCO Finland

Flexible sigmoidoscopy with biopsy

1.7

6.5

118

698

N40

ICD-10 Finland

Hyperplasia of prostate

1.4

6.4

290

2146

N30.0

ICD-10 Finland

Acute cystitis

1.6

6.3

181

1209

R07.4

ICD-10 Finland

Chest pain, unspecified

1.4

6.3

364

2812

A09

ICD-10 Finland

Other gastroenteritis and colitis of infectious and unspecified origin

1.5

6.3

195

1332

205

Kela drug reimbursment

Chronic hypertension

1.4

6.2

418

3310

M03BC01

ATC

orphenadrine (citrate); systemic

1.4

6.2

265

1936

J01CA04

ATC

amoxicillin; systemic

1.3

6.1

1051

9560

H02AB06

ATC

prednisolone; systemic

1.3

6.1

617

5197

D06

ICPC

Abdominal pain localized other

1.8

6.1

103

594

G04BD12

ATC

mirabegron; oral

1.6

6.1

141

891

WX704

NOMESCO Finland

Intubation

1.9

6.1

482

SDE03

NOMESCO Finland

Periodontal treatment by dental hygienist, extensive

1.4

6.1

279

2066

L15

ICPC

Knee symptom/complaint

1.4

6.1

263

1924

D41.3

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Urethra

12.6

6.1

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_BENIGN_URINARY and mortality.

Females

Parameter	HR [95% CI]	p-value
CD2_BENIGN_URINARY	1.337 [1.19, 1.5]	< 0.001
Birth year	0.996 [0.99, 1.0]	0.32

During the follow-up period (1.1.1998 — 31.12.2019), 899 out of 4105 females with CD2_BENIGN_URINARY died.

Males

Parameter	HR [95% CI]	p-value
CD2_BENIGN_URINARY	1.422 [1.26, 1.61]	< 0.001
Birth year	0.991 [0.98, 1.0]	0.059

During the follow-up period (1.1.1998 — 31.12.2019), 1092 out of 3120 males with CD2_BENIGN_URINARY died.

Mortality risk

Mortality risk for people of age

years, who have CD2_BENIGN_URINARY.

N-year risk	Females	Males
1	0.09%	0.272%
5	0.73%	1.823%
10	1.935%	4.401%
15	3.666%	8.57%
20	6.835%	14.215%

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_URINARY – Benign neoplasm of urinary organs

GWS hits: 1

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

Extremity

rg [CI]

Extremity

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

NAME	CD2_BENIGN_URINARY
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE	CD2_BENIGN_KIDNEY\|CD2_BENIGN_RENALPELVIS\|CD2_BENIGN_URETER\|CD2_BENIGN_BLADDER\|CD2_BENIGN_URETHRA\|CD2_BENIGN_URINARY_NOS
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D30
HD_ICD_9
HD_ICD_8
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	D30
COD_ICD_9
COD_ICD_8
COD_ICD_10_EXCL
COD_ICD_9_EXCL
COD_ICD_8_EXCL
OPER_NOM
OPER_HL
OPER_HP1
OPER_HP2
KELA_REIMB
KELA_REIMB_ICD
KELA_ATC_NEEDOTHER
KELA_ATC
KELA_VNRO_NEEDOTHER
KELA_VNRO
CANC_TOPO
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

Benign neoplasm of urinary organs

Endpoint definition

Endpoint definition steps

FinnGen

Phenotype data

1. Apply sex-specific rule

2. Check conditions

3. Check pre-conditions, main-only, mode, registry filters

4. Check minimum number of events

5. Include endpoints

6. Filter based on genotype QC (FinnGen only)

Similar endpoints

Case counts by codes

Summary Statistics

-FinRegistry-

Key figures

-FinnGen-

Key figures

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

Matched cohort

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints