Risteys · CD2_BENIGN_OTHER

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 — D36 Cause of death: ICD-10 — D36 2 out of 7 registries used, show all original rules.	903
4. Check minimum number of events None	903
5. Include endpoints CD2_BENIGN_LYMPHNODES CD2_BENIGN_PERIPH_AUTO_NEURO CD2_BENIGN_NOS	1191
6. Filter based on genotype QC (FinnGen only)	1191

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	9119	5174	3872
Only index persons	7706	4485	3221
Unadjusted period prevalence (%)
Whole population	0.13	0.15	0.11
Only index persons	0.15	0.16	0.12
Median age at first event (years)
Whole population	50.01	50.24	49.59
Only index persons	47.98	48.44	47.33

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	1191	695	496
Unadjusted period prevalence (%)	0.23	0.24	0.22
Median age at first event (years)	49.14	47.16	51.91

-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
1071: Matched controls
10709

Code

Vocabulary

Description

Odds Ratio

-log₁₀(p)

N matched cases

N matched controls

D36.7

ICD-10 Finland

Benign neoplasm: Other specified sites

1689.2

323.0

345

D36.1

ICD-10 Finland

Benign neoplasm: Peripheral nerves and autonomic nervous system

+∞

323.0

338

22899

ICD-8 Finland

Benign neoplasm of other and unspecified organs and tissues

+∞

108.2

102

22550

ICD-8 Finland

Benign neoplasm of brain and other parts of nervous system, Peripheral nerves

+∞

102.8

D36.0

ICD-10 Finland

Benign neoplasm: Lymph nodes

+∞

88.8

ACB19

NOMESCO Finland

Excision of lesion of peripheral nerve other or unspecified

313.9

58.9

D36.9

ICD-10 Finland

Benign neoplasm: Benign neoplasm of unspecified site

599.2

58.2

2258X

ICD-9 Finland

Benign neoplasm of brain and other parts of nervous system, Other specified sites of nervous system

+∞

55.7

DHB10

NOMESCO Finland

Excision of lesion of internal nose

42.6

30.1

Q85.00

ICD-10 Finland

Neurofibromatosis, type 1

107.0

19.6

Q85.09

ICD-10 Finland

Unspecified neurofibromatosis

107.0

19.6

D48.1

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Connective and other soft tissue

6.3

18.8

D48.2

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Peripheral nerves and autonomic nervous system

193.2

18.6

D33.45

ICD-10 Finland

Benign Schwannom in the nerve root of the spinal cord

27.2

17.9

DHB00

NOMESCO Finland

Excision of lesion of external nose

12.2

17.4

2401

FHL

Nerve exploration (includes biopsy and removal of local change)

40.7

16.4

DHA10

NOMESCO Finland

Biopsy of cavity of nose

9.9

15.2

D14.0

ICD-10 Finland

Benign neoplasm: Middle ear, nasal cavity and accessory sinuses

9.9

15.2

QAE10

NOMESCO Finland

Excision of other lesion extending through all layers of skin in head or neck

2.5

15.0

119

501

ACB99

NOMESCO Finland

Other operation for lesion of peripheral nerve: other or unspecified

+∞

14.6

N03AX16

ATC

pregabalin; oral

1.9

14.6

274

1675

AA1CG

NOMESCO Finland

Extensive MRI examination of brain with high intensity magnet

2.7

13.8

100

400

D48.9

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Neoplasm of uncertain or unknown behaviour, unspecified

5.7

13.4

NDR20

NOMESCO Finland

Incomplete excision of soft tissue tumour of wrist or hand

6.8

13.3

R22.4

ICD-10 Finland

Localized swelling, mass and lump, lower limb

4.6

13.3

104

9560/0-C72.9

ICD-O-3

Schwannoma, NOS, of nervous system, NOS

+∞

12.5

Q85.0

ICD-10 Finland

Neurofibromatosis (nonmalignant)

131.5

12.5

WX408

NOMESCO Finland

General anesthesy, balanced

1.7

12.2

288

1881

N03AX12

ATC

gabapentin; oral

2.0

12.0

176

978

ZXA05

NOMESCO Finland

Left side

1.7

10.5

277

1854

ZXA00

NOMESCO Finland

Right side

1.7

10.3

283

1913

ZXD10

NOMESCO Finland

Scheduled procedure

1.6

10.2

403

2991

D21.2

ICD-10 Finland

Benign neoplasm: Connective and other soft tissue of lower limb, including hip

13.3

10.2

R22.3

ICD-10 Finland

Localized swelling, mass and lump, upper limb

4.7

9.4

2899X

ICD-9 Finland

Other diseases of blood and blood-forming organs, Unspecified diseases of blood and blood-forming organs

+∞

9.4

R10.4

ICD-10 Finland

Other and unspecified abdominal pain

1.5

9.2

349

2547

QBE10

NOMESCO Finland

Excision of other lesion extending through all layers of skin of trunk

2.3

9.2

361

D17.2

ICD-10 Finland

Benign lipomatous neoplasm of skin and subcutaneous tissue of limbs

4.1

9.2

EP1CG

NOMESCO Finland

Extensive MRI examination of soft tissue of neck with high intesity magnet

6.0

9.1

EP1AE

NOMESCO Finland

Neck ultrasound examination

2.5

9.1

286

QDE10

NOMESCO Finland

Excision of other lesion extending through all layers of skin in lower limb

3.1

9.1

165

NA3BG

NOMESCO Finland

Lumbar spine MRI examination with high intensity magnet

2.1

9.0

107

545

R22.9

ICD-10 Finland

Localized swelling, mass and lump, unspecified

2.3

8.9

366

S18

ICPC

Laceration/cut

1.5

8.8

415

3175

WX110

NOMESCO Finland

Local anesthesy

1.5

8.7

688

5864

R03AC02

ATC

salbutamol; inhalant

1.5

8.6

515

4140

Q85.01

ICD-10 Finland

Neurofibromatosis, type 2

90.7

8.4

ZXE10

NOMESCO Finland

More than one and less than three hours

1.5

8.4

374

2820

ABB00

NOMESCO Finland

Excision of lesion of spinal canal

12.9

8.4

ACB15

NOMESCO Finland

Excision of local lesion of tibial nerve

+∞

8.3

NA3CG

NOMESCO Finland

Lumbar spine extensive MRI examination with high intensity magnet

2.9

8.3

175

R51

ICD-10 Finland

Headache

2.7

8.3

206

R22.2

ICD-10 Finland

Localized swelling, mass and lump, trunk

3.2

8.2

131

R51.80

ICD-10 Finland

Headache

1.8

8.2

142

830

D48.0

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Bone and articular cartilage

5.2

8.2

WX404

NOMESCO Finland

Intravenous generell anesthesy

1.6

8.1

210

1385

N02BE01

ATC

paracetamol; systemic, rectal

1.6

8.1

887

8043

D48.5

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Skin

2.4

8.1

278

D33.30

ICD-10 Finland

Acoustic neuroma

10.1

8.0

NK1AT

NOMESCO Finland

Muscle biopsy with ultrasound guidance

13.1

7.9

R22.1

ICD-10 Finland

Localized swelling, mass and lump, neck

2.8

7.9

176

R10.3

ICD-10 Finland

Pain localized to other parts of lower abdomen

1.6

7.7

194

1272

A02BC03

ATC

lansoprazole; oral

1.5

7.7

294

2134

UDH02

NOMESCO Finland

Rhinopharyngoscopy

2.2

7.6

353

M79.6

ICD-10 Finland

Pain in limb

1.5

7.6

344

2590

WX302

NOMESCO Finland

Thoracal epidural anesthesy

2.4

7.6

268

PJA10

NOMESCO Finland

Exploration of lymph nodes

5.5

7.5

NA1CG

NOMESCO Finland

Cervical spine extensive MRI examination with high intensity magnet

4.2

7.5

D21.1

ICD-10 Finland

Benign neoplasm: Connective and other soft tissue of upper limb, including shoulder

5.3

7.4

D23.3

ICD-10 Finland

Benign neoplasm: Skin of other and unspecified parts of face

3.2

7.4

114

Z31.5

ICD-10 Finland

Genetic counselling

2.5

7.3

228

ACB18

NOMESCO Finland

Excision of local lesion of brachial plexus

+∞

7.3

N02AX02

ATC

tramadol; systemic, rectal

1.4

7.2

416

3282

SPAT1153

SPAT

Removal of sutures

1.5

6.9

314

2359

A02BC02

ATC

pantoprazole; systemic

1.4

6.9

639

5483

R59.1

ICD-10 Finland

Generalized enlarged lymph nodes

4.7

6.7

P01AB01

ATC

metronidazole; oral, rectal

1.4

6.7

386

3030

ABD30

NOMESCO Finland

Implantation of spinal stimulation device

6.5

6.6

NA3EA

NOMESCO Finland

Lumbar spine X-ray examination with flexion

2.9

6.6

133

A02BC05

ATC

esomeprazole; systemic

1.4

6.6

395

3124

UJF32

NOMESCO Finland

Coloscopy

1.5

6.6

248

1785

GD1AA

NOMESCO Finland

Thorax X-ray examination

1.4

6.6

424

3397

NA7CG

NOMESCO Finland

Spine and spinal cord extensive MRI examination with high intensity magnet

5.4

6.5

M01AC06

ATC

meloxicam; systemic, rectal

1.4

6.5

349

2705

R07.4

ICD-10 Finland

Chest pain, unspecified

1.5

6.4

252

1834

NA2CG

NOMESCO Finland

Thoracal spine extensive MRI examination with high intensity magnet

6.0

6.3

D21.9

ICD-10 Finland

Benign neoplasm: Connective and other soft tissue, unspecified

18.1

6.3

Q85.1

ICD-10 Finland

Tuberous sclerosis

+∞

6.3

FB1BD

NOMESCO Finland

Extensive CT examination of arteria pulmonalis

2.0

6.2

364

J01.0

ICD-10 Finland

Acute maxillary sinusitis

1.5

6.2

193

1332

QX2XE

NOMESCO Finland

Ultrsound examination of soft tissue not elsewhere classified

2.8

6.1

137

WZB00

NOMESCO Finland

Telephone receipt or other advice

1.5

6.1

259

1910

D37.6

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Liver, gallbladder and bile ducts

4.2

6.0

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_BENIGN_OTHER_NOS and mortality.

Females

Parameter	HR [95% CI]	p-value
CD2_BENIGN_OTHER_NOS	1.242 [1.09, 1.41]	< 0.001
Birth year	0.991 [0.98, 1.0]	0.039

During the follow-up period (1.1.1998 — 31.12.2019), 549 out of 2966 females with CD2_BENIGN_OTHER_NOS died.

Males

Parameter	HR [95% CI]	p-value
CD2_BENIGN_OTHER_NOS	1.366 [1.18, 1.57]	< 0.001
Birth year	0.985 [0.98, 1.0]	0.004

During the follow-up period (1.1.1998 — 31.12.2019), 531 out of 2412 males with CD2_BENIGN_OTHER_NOS died.

Mortality risk

Mortality risk for people of age

years, who have CD2_BENIGN_OTHER_NOS.

N-year risk	Females	Males
1	0.159%	0.289%
5	0.643%	1.611%
10	1.644%	3.828%
15	3.185%	6.966%
20	5.527%	11.602%

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_OTHER_NOS – Benign neoplasm of other and unspecified sites

GWS hits: 3

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_OTHER_NOS
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE	CD2_BENIGN_LYMPHNODES\|CD2_BENIGN_PERIPH_AUTO_NEURO\|CD2_BENIGN_NOS
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D36
HD_ICD_9
HD_ICD_8
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	D36
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 other and unspecified sites

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