Background
Methods
Study population
Diagnosis of ICASO
FastTarget sequencing
Variant filtration
Statistical analysis
Result
Characteristics of participants
Characteristics | ICASO(n = 250) |
---|---|
Age(years) | |
Mean ± SD [Range] | 57.8 ± 8.6 [28–70] |
Female, n(%) | 77(30.8) |
Risk factors, n(%) | |
Smoking | 97(38.8) |
Drinking | 63(25.2) |
Hypertension | 152(60.8) |
Diabetes | 60(24.0) |
Hyperlipemia | 95(38.0) |
Clinical symptoms, n(%) | |
Hemorrhage | 7(2.8) |
Infarction | 165(66.0) |
Ischemia | 77(30.8) |
Other | 9(3.6) |
Multiple stenosis | 199(79.6) |
Location | |
Anterior circulationa | 36(14.4) |
Posterior circulationb | 99(39.6) |
Multiple circulationc | 111(44.4) |
Others | 4(1.6) |
Identification of low frequency and rare variants in target region
Filtration Steps | Number of variants | ||
---|---|---|---|
1.SNVsa located in exonic/ splicing region | 188 | ||
2. Nonsynonymous SNVs/ frameshift deletion/ stopgain | 125 | ||
3. Variants judged as SIFT prediction = Damaging / unknown and PolyPhen-2 prediction = Possibly damaging/ Probably damaging/ Unknown | 71 | ||
4. MAF < 0.05 in 1KGP(Chinese Han population) and GeneSky in-house Database | 42 | ||
5.Variants with sequenced base depth > 10x | 18 | ||
Result of RNF213 gene-based analysis | |||
MAF | PWSS | PSKAT | PSKAT-O |
< 0.05 | 4.88 × 10−10 | 9.68 × 10−6 | 3.42 × 10−9 |
< 0.01 | 4.56 × 10−12 | 2.80 × 10−6 | 3.20 × 10−11 |
Position | Gene Region | Function | Varianta | SNP ID | Genotypeb | SIFTc | POLYPhen V2c | |||
---|---|---|---|---|---|---|---|---|---|---|
cDNA | Amino Acid | Case | 1000G_CHB | GENESKY | ||||||
Chr17:78247076–78,247,076 | exonic | frameshift | c.134delC | p.S45 fs | – | 249/1/0 | 208/0/0 | 1007/0/0 | – | – |
Chr17:78298891 | exonic | missense | c.3086 T > C | p.L1029S | rs753208141 | 249/1/0 | 208/0/0 | 1007/0/0 | D | D |
Chr17:78307986 | exonic | missense | c.4225G > T | p.D1409Y | – | 249/1/0 | 208/0/0 | 1007/0/0 | D | D |
Chr17:78311532 | splicing | – | c.4668 + 6C > T | – | rs78795452 | 248/2/0 | 205/3/0 | 1007/0/0 | – | – |
Chr17:78311620 | splicing | – | c.4669-13A > G | – | rs750893752 | 249/1/0 | 208/0/0 | 999/8/0 | – | – |
Chr17:78313764 | exonic | missense | c.5597C > T | p.T1866I | rs546687179 | 244/6/0 | 207/1/0 | 1007/0/0 | D | – |
Chr17:78318465 | splicing | – | c.6343-13C > G | – | rs141121193 | 246/4/0 | 206/2/0 | 992/15/0 | – | – |
Chr17:78319385 | exonic | missense | c.7250 T > G | p.I2417S | rs181965032 | 244/6/0 | 201/7/0 | 992/15/0 | D | P |
Chr17:78326772 | exonic | missense | c.10336C > T | p.R3446W | rs776943470 | 249/1/0 | 208/0/0 | 992/15/0 | D | D |
Chr17:78350088 | splicing | – | c.13186-13 T > C | – | rs113236556 | 239/11/0 | 202/6/0 | 1006/1/0 | – | – |
Chr17:78353469 | exonic | missense | c.13595 T > C | p.I4532T | rs373648166 | 249/1/0 | 208/0/0 | 975/32/0 | D | D |
Chr17:78354738 | exonic | missense | c.13748G > A | p.R4583Q | rs199887580 | 249/1/0 | 208/0/0 | 1007/0/0 | D | D |
Chr17:78355494 | exonic | missense | c.13945C > G | p.L4649 V | rs61745599 | 249/1/0 | 208/0/0 | 1007/0/0 | D | D |
Chr17:78356830 | exonic | missense | c.14030G > T | p.W4677 L | rs61741961 | 249/1/0 | 208/0/0 | 1006/1/0 | D | D |
Chr17:78357541 | exonic | missense | c.14135A > T | p.N4712I | – | 249/1/0 | 208/0/0 | 1007/0/0 | D | D |
Chr17:78360656 | exonic | missense | c.14887C > T | p.R4963C | rs772035323 | 249/1/0 | 208/0/0 | 1007/0/0 | D | D |
Chr17:78362497 | splicing | – | c.15000 + 8C > T | – | – | 249/1/0 | 208/0/0 | 1006/1/0 | – | – |
Chr17:78363181 | splicing | – | c.15195 + 14C > T | – | rs373144473 | 249/1/0 | 208/0/0 | 1007/0/0 | – | – |
Distribution of rare variants in ICASO patients and gene-based association test
Variant | Ref | Alt | Case_Ref | Case_Alt | Control_Ref | Control_Alt | OR | 95%CI | p value* |
---|---|---|---|---|---|---|---|---|---|
Chr17:78247076–78,247,076 | C | – | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78298891 | T | C | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78307986 | G | T | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78311532 | C | T | 498 | 2 | 2419 | 11 | 0.88 | (0.20–4.00) | 1.000 |
Chr17:78311620 | A | G | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78313764 | C | T | 494 | 6 | 2414 | 16 | 1.83 | (0.71–4.71) | 0.248 |
Chr17:78318465 | C | G | 496 | 4 | 2403 | 27 | 0.72 | (0.25–2.06) | 0.383 |
Chr17:78319385 | T | G | 494 | 6 | 2408 | 22 | 1.33 | (0.54–3.30) | 0.716 |
Chr17:78326772 | C | T | 499 | 1 | 2429 | 1 | 4.87 | (0.30–77.95) | 0.312 |
Chr17:78350088 | T | C | 489 | 11 | 2392 | 38 | 1.42 | (0.72–2.79) | 0.312 |
Chr17:78353469 | T | C | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78354738 | G | A | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78355494 | C | G | 499 | 1 | 2429 | 1 | 4.87 | (0.30–77.95) | 0.312 |
Chr17:78356830 | G | T | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78357541 | A | T | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78360656 | C | T | 499 | 1 | 2429 | 1 | 4.87 | (0.30–77.95) | 0.312 |
Chr17:78362497 | C | T | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Chr17:78363181 | C | T | 499 | 1 | 2430 | 0 | – | – | 0.171 |
Total counts | 8958 | 42 | 43,623 | 117 | 1.74 | (1.23–2.49) | 0.002 |
Clinical characteristics of patients with and without RNF213 rare variants
Characteristics | Carrier(n = 39) | Non-carrier(n = 211) | p value |
---|---|---|---|
Age(years) | |||
Mean ± SD | 60.5 ± 6.2 | 57.3 ± 8.9 | 0.028 |
Female, n(%) | 12(30.8) | 65(30.8) | 0.996 |
Risk factors, n(%) | |||
Smoking | 16(41.0) | 81(38.4) | 0.756 |
Drinking | 14(35.9) | 49(23.2) | 0.095 |
Hypertension | 29(74.4) | 123(58.3) | 0.059 |
Diabetes | 12(30.8) | 48(22.7) | 0.281 |
Hyperlipemia | 14(35.9) | 81(38.4) | 0.768 |
Clinical symptoms, n(%) | |||
Hemorrhage | 3(7.7) | 4(1.9) | 0.137 |
Infarction | 29(74.4) | 136(64.5) | 0.23 |
Ischemia | 8(20.5) | 69(32.7) | 0.13 |
Other | 1(2.6) | 8(3.8) | |
Characteristics of cerebral artery stenosis, n(%) | |||
Multiple stenosis | 29(74.4) | 170(80.6) | 0.377 |
Location | |||
Anterior circulationa | 4(10.3) | 32(15.2) | 0.688 |
Posterior circulationb | 14(35.9) | 85(40.3) | |
Multiple circulationc | 20(51.3) | 91(43.1) | |
Others | 1(2.6) | 3(1.4) |