Lab Med Qual Assur 2022; 44(2): 61-75
Published online June 30, 2022
https://doi.org/10.15263/jlmqa.2022.44.2.61
Copyright © Korean Association of External Quality Assessment Service.
Heerah Lee , Boram Kim
, Man Jin Kim
, Jee-Soo Lee
, Sung Im Cho
, Ho Seop Shin
, and Moon-Woo Seong
Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
Correspondence to:Moon-Woo Seong
Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
Tel +82-2-2072-4180
E-mail MWSeong@snu.ac.kr
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
The human genetics molecular diagnostic proficiency testing program of the Korean Association of Quality Assurance for Clinical Laboratory conducted two trials annually from 2018–2021. The program consisted of the same 20 test items throughout the four year period while the number of participating laboratories fluctuated depending on the test item. The survey included hereditary breast and ovarian cancer genes (BRCA1 and BRCA2), Li-Fraumeni syndrome (TP53), Wilson disease (ATP7B), achondroplasia (FGFR3), hearing loss and deafness (GJB2), Avellino type corneal dystrophy (TGFBI), multiple endocrine neoplasia 2 (RET), Huntington’s disease, spinocerebellar ataxia, spinal and bulbar muscular atrophy, mitochondrial encephalopathy with lactic acidosis and stroke-like episodes, myoclonic epilepsy with ragged red fibers, Leber hereditary optic neuropathy, Prader-Willi and Angelman syndrome, Duchenne muscular dystrophy, spinal muscular atrophy, fragile X syndrome, apolipoprotein E genotyping, methylenetetrahydrofolate reductase genotyping, and ABO genotyping. The survey showed high confidence levels and improved overall performance. A method-based proficiency test survey for molecular diagnostic testing serves as a useful approach to assess the performance of clinical laboratories.
Keywords: Laboratory proficiency testing, Molecular pathology, Molecular genetics, Molecular biology
2018년부터 2021년까지 유전질환 진단유전검사와 기타 진단유전검사 신빙도조사는 전체 회원기관에게 참가신청 조사를 하여 매년 2회 시행하였다. 유전질환 진단유전검사는 20종의 유전질환 및 유전자 항목에 대해 다양한 유전변이를 포함하도록 구성하여 회차별 2종의 DNA 검체를 참여기관에 배포하였다. 기타 진단유전검사는 ABO 유전형 검사항목에 대해 다양한 조합의 유전형을 구성하여 2종의 DNA 검체로 배포하였다.
신빙도조사는 매해 상반기에 1회, 하반기에 1회 시행하였다. 신빙도조사 항목의 매년 회차별 검체와 검체번호, 예상결과, 전체 참여기관 수, 예상결과와 일치하는 보고를 한 기관 수는 Table 1과 같다. 신빙도조사 항목별로 각 기관의 검사방법을 조사하였고, 이에 따라 검사방법별로 검사결과를 비교 분석하였다. 신빙도조사 항목별로 참여기관의 보고결과를 acceptable 혹은 unacceptable로 평가하였다. Acceptable 및 unacceptable의 기준은 참여기관의 수가 10개 기관 이상인 경우와 미만인 경우로 구분하여 설정하였다. 참여기관이 10개 기관 이상인 경우 참여기관 중에서 80% 이상의 일치가 있을 경우, 일치된 결과를 기준으로 평가하였고, 10개 기관 미만인 경우 주관기관의 예상결과를 기준으로 평가하였다. 삼염기 반복 유전질환인 Huntington’s disease (HD), spinocerebellar ataxia (SCA1, SCA2, SCA3, SCA6, SCA7), spinal and bulbar muscular atrophy (SBMA), fragile X syndrome (FMR1) 검사의 경우, 정성적 결과를 평가에 포함하였지만 정량적 결과는 평가에 포함시키지 않고 참여기관의 분포를 통계값으로 제시하였다.
Table 1 . Results of the molecular diagnostics test survey carried out in 2018–2021.
Tests | S* | Intended responses | T/A |
---|---|---|---|
2018 1st trials | |||
ABO genotype | 18-01 | cis-AB/O genotype | 12/12 |
18-02 | A/O genotype | 12/12 | |
BRCA1 | 18-01 | c.3627dup, p.Glu1210Argfs*9, heterozygote | 19/19 |
18-02 | No variant | 19/18 | |
BRCA2 | 18-03 | No variant | 19/18 |
18-04 | c.1399A>T, p.Lys467*, heterozygote | 19/18 | |
TP53 | 18-05 | c.742C>T, p.Arg248Trp, heterozygote | 6/6 |
18-06 | No variant | 6/6 | |
ATP7B | 18-07 | Probably not Wilson disease | 8/8 |
18-08 | c.2310C>G, p.Leu770=, heterozygote(;)c.2333G>T, p.Arg778Leu, heterozygote | 8/8 | |
MT-TL1 | 18-09 | m.3243A>G | 6/6 |
18-10 | No variant | 6/6 | |
MT-TK | 18-11 | No variant | 5/5 |
18-12 | m.8344A>G | 5/5 | |
GJB2 | 18-13 | No variant | 11/11 |
18-14 | c.35del, p.Gly12Valfs*2, heterozygote | 11/10 | |
LHON | 18-15 | m.14484T>C | 6/5 |
18-16 | No variant | 6/6 | |
RET | 18-17 | No variant | 8/8 |
18-18 | c.2410G>A, p.Val804Met, heterozygote | 8/8 | |
SCA | 18-19 | Normal (no risk of SCA) | 7/7 |
18-20 | Positive, SCA causing allele with full penetrance | 7/6 | |
APOE genotype | 18-21 | APOE ε3/ε3 genotype | 40/40 |
18-22 | APOE ε4/ε4 genotype | 40/40 | |
Achondroplasia | 18-23 | FGFR3, G380R mutation, negative | 8/8 |
18-24 | FGFR3, G380R mutation, positive | 8/8 | |
MTHFR genotype | 18-25 | MTHFR 677T/T homozygous genotype | 15/15 |
18-26 | Homozygous normal (wild type/wild type) | 15/15 | |
PWS/AS | 18-27 | Normal methylation pattern | 5/5 |
18-28 | Angelman syndrome | 5/5 | |
DMD | 18-29 | No deletion/duplication | 6/6 |
18-30 | Exon 45-53 deletion | 6/6 | |
HD | 18-31 | No risk of HD | 5/5 |
18-32 | Full penetrance | 5/5 | |
FMR1 | 18-33 | Full mutation | 11/10 |
18-34 | No expansion | 11/11 | |
TGFBI | 18-35 | TGFBI, R124H mutation, positive | 15/15 |
18-36 | TGFBI, R124H mutation, negative | 15/15 | |
SBMA | 18-37 | No risk of SBMA | 5/5 |
18-38 | Full penetrance | 5/5 | |
SMA | 18-39 | Reduced probability of SMA | 7/7 |
18-40 | SMN1, Exon7, homozygous deletion | 7/7 | |
2018 2nd trials | |||
ABO genotype | 18-03 | B/O genotype | 12/12 |
18-04 | cis-AB/O genotype | 12/12 | |
BRCA1 | 18-41 | No variant | 19/17 |
18-42 | c.3756_3759del, p.Ser1253Argfs*10, heterozygote | 19/18 | |
BRCA2 | 18-43 | c.5576_5579del, p.Ile1859Lysfs*3, heterozygote | 19/19 |
18-44 | No variant | 19/19 | |
TP53 | 18-45 | No variant | 6/6 |
18-46 | c.742C>T, P.Arg248Trp, heterozygote | 6/5 | |
ATP7B | 18-47 | c.2310C>G, p.Leu770=, heterozygote(;)c.2333G>T, p.Arg778Leu, heterozygote(;)c.3247C>T, p.Leu1083Phe, heterozygote | 8/8 |
18-48 | Probably not Wilson disease | 8/8 | |
MT-TL1 | 18-49 | No variant | 6/6 |
18-50 | m.3243A>G | 6/6 | |
MT-TK | 18-51 | m.8344A>G | 5/5 |
18-52 | No variant | 5/5 | |
GJB2 | 18-53 | c.35del, p.Gly12Valfs*2, heterozygote | 11/10 |
18-54 | No variant | 11/11 | |
LHON | 18-55 | No variant | 6/6 |
18-56 | m.4171C>A | 6/4 | |
RET | 18-57 | c.2410G>A, p.Val804Met, heterozygote | 7/7 |
18-58 | No variant | 7/7 | |
SCA | 18-59 | Positive, SCA causing allele with full penetrance | 7/7 |
18-60 | Normal (no risk of SCA) | 7/7 | |
APOE genotype | 18-61 | APOE ε4/ε4 genotype | 42/42 |
18-62 | APOE ε3/ε4 genotype | 42/42 | |
Achondroplasia | 18-63 | FGFR3, G380R mutation, positive | 8/8 |
18-64 | FGFR3, G380R mutation, negative | 8/8 | |
MTHFR genotype | 18-65 | MTHFR 677C/T heterozygous genotype | 15/15 |
18-66 | MTHFR 677T/T homozygous genotype | 15/15 | |
PWS/AS | 18-67 | Prader-Willi syndrome | 5/5 |
18-68 | Normal methylation pattern | 5/5 | |
DMD | 18-69 | Exon 2-44 deletion | 6/5 |
18-70 | No deletion/duplication | 6/5 | |
HD | 18-71 | Full penetrance | 5/5 |
18-72 | No risk of HD | 5/5 | |
FMR1 | 18-73 | No expansion | 11/11 |
18-74 | Full mutation | 11/10 | |
TGFBI | 18-75 | TGFBI, R124H mutation, negative | 16/16 |
18-76 | TGFBI, R124H mutation, positive | 16/16 | |
SBMA | 18-77 | Full penetrance | 5/5 |
18-78 | No risk of SBMA | 5/5 | |
SMA | 18-79 | SMN1, Exon7, homozygous deletion | 7/7 |
18-80 | Reduced probability of SMA | 7/7 | |
2019 1st trials | |||
ABO genotype | 19-01 | A/O genotype | 13/12 |
19-02 | A/O genotype | 13/13 | |
BRCA1 | 19-01 | c.2157dup, p.Glu720Argfs*6, heterozygote | 24/19 |
19-02 | No variant | 24/18 | |
BRCA2 | 19-03 | c.755_758del, p.Asp252Valfs*24, heterozygote | 24/24 |
19-04 | No variant | 24/24 | |
TP53 | 19-05 | c.722C>T, p.Ser241Phe, heterozygote | 7/7 |
19-06 | No variant | 7/7 | |
ATP7B | 19-07 | c.3191A>C, p.Glu1064Ala, heterozygote(;)c.3207C>A, p.His1069Gln, heterozygote | 8/8 |
19-08 | Probably not Wilson disease | 8/8 | |
MT-TL1 | 19-09 | No variant | 6/5 |
19-10 | No variant | 6/6 | |
MT-TK | 19-11 | m.8344A>G | 5/5 |
19-12 | No variant | 5/5 | |
GJB2 | 19-13 | Ungraded | 11 |
19-14 | No variant | 10/10 | |
LHON | 19-15 | m.11778G>A | 5/5 |
19-16 | No variant | 5/5 | |
RET | 19-17 | c.2753T>C, p.Met918Thr, heterozygote | 7/7 |
19-18 | No variant | 7/7 | |
SCA | 19-19 | Positive, SCA causing allele with full penetrance | 7/3 |
19-20 | Normal (no risk of SCA) | 7/7 | |
APOE genotype | 19-21 | APOE ε3/ε3 genotype | 46/46 |
19-22 | APOE ε3/ε3 genotype | 46/46 | |
Achondroplasia | 19-23 | FGFR3, G380R mutation, positive | 8/8 |
19-24 | FGFR3, G380R mutation, negative | 8/8 | |
MTHFR genotype | 19-25 | MTHFR 677C/T heterozygous genotype | 16/16 |
19-26 | MTHFR 677C/T heterozygous genotype | 16/16 | |
PWS/AS | 19-27 | Prader-Willi syndrome | 6/6 |
19-28 | Normal methylation pattern | 6/6 | |
DMD | 19-29 | Exon 45 deletion | 6/6 |
19-30 | No deletion/duplication | 6/6 | |
HD | 19-31 | Full penetrance | 6/6 |
19-32 | No risk of HD | 6/4 | |
FMR1 | 19-33 | Full mutation | 10/10 |
19-34 | No expansion | 10/8 | |
TGFBI | 19-35 | TGFBI, R124H mutation, negative | 15/15 |
19-36 | TGFBI, R124H mutation, negative | 15/15 | |
SBMA | 19-37 | Full penetrance | 5/5 |
19-38 | No risk of SBMA | 5/5 | |
SMA | 19-39 | SMN1, Exon7, homozygous deletion | 8/8 |
19-40 | SMN1, Exon7, heterozygous deletion | 8/5 | |
2019 2nd trials | |||
ABO genotype | 19-03 | A/O genotype | 14/14 |
19-04 | A/O genotype | 14/14 | |
BRCA1 | 19-41 | c.798_799del, p.Ser267Lysfs*19, heterozygote | 23/23 |
19-42 | No variant | 23/23 | |
BRCA2 | 19-43 | c.6198_6199del, p.Ser2067Hisfs*10, heterozygote | 23/23 |
19-44 | No variant | 23/23 | |
TP53 | 19-45 | c.743G>A, p.Arg248Gln, heterozygote | 6/6 |
19-46 | No variant | 6/6 | |
ATP7B | 19-47 | c.3191A>C, p.Glu1064Ala, heterozygote(;)c.3207C>A, p.His1069Gln, heterozygote | 7/6 |
19-48 | Probably not Wilson disease | 7/7 | |
MT-TL1 | 19-49 | No variant | 4/4 |
19-50 | No variant | 4/4 | |
MT-TK | 19-51 | No variant | 3/3 |
19-52 | No variant | 3/3 | |
GJB2 | 19-53 | c.35del, p.Gly12Valfs*2, heterozygote | 9/8 |
19-54 | No variant | 9/9 | |
LHON | 19-55 | m.11778G>A | 3/3 |
19-56 | m.3460G>A | 3/3 | |
RET | 19-57 | c.1859G>T, p.Cys620Phe, heterozygote | 5/5 |
19-58 | No variant | 5/5 | |
SCA | 19-59 | Normal (no risk of SCA) | 4/4 |
19-60 | Positive, SCA causing allele with full penetrance | 4/4 | |
APOE genotype | 19-61 | APOE ε3/ε4 genotype | 44/44 |
19-62 | APOE ε3/ε4 genotype | 44/44 | |
Achondroplasia | 19-63 | FGFR3, G380R mutation, positive | 6/6 |
19-64 | FGFR3, G380R mutation, negative | 6/6 | |
MTHFR genotype | 19-65 | MTHFR 677C/T heterozygous genotype | 15/15 |
19-66 | Homozygous normal (wild type/wild type) | 15/15 | |
PWS/AS | 19-67 | Angelman syndrome | 4/4 |
19-68 | Normal methylation pattern | 4/4 | |
DMD | 19-69 | Exon 45 deletion | 4/4 |
19-70 | No deletion/duplication | 3/3 | |
HD | 19-71 | Full penetrance | 4/4 |
19-72 | Full penetrance | 4/4 | |
FMR1 | 19-73 | Full mutation | 8/8 |
19-74 | No expansion | 8/8 | |
TGFBI | 19-75 | TGFBI, R124H mutation, negative | 13/13 |
19-76 | TGFBI, R124H mutation, negative | 13/13 | |
SBMA | 19-77 | Full penetrance | 3/3 |
19-78 | No risk of SBMA | 3/3 | |
SMA | 19-79 | SMN1, Exon7, homozygous deletion | 6/6 |
19-80 | Reduced probability of SMA | 6/6 | |
2020 1st trials | |||
ABO genotype | 20-01 | A/O genotype | 16/16 |
20-02 | O/O genotype | 16/16 | |
BRCA1 | 20-01 | c.2071del, p.Arg691Aspfs*10, heterozygote(;)c.2082C>T, p.Ser694=, heterozygote | 25/25 |
20-02 | No variant | 25/25 | |
BRCA2 | 20-03 | c.9976A>T, p.Lys3326*, heterozygote | 25/21 |
20-04 | No variant | 25/25 | |
TP53 | 20-05 | c.476C>T, p.Ala159Val, homozygote | 8/8 |
20-06 | No variant | 8/8 | |
ATP7B | 20-07 | c.3191A>C, p.Glu1064Ala, heterozygote(;)c.3207C>A, p.His1069Gln, heterozygote | 9/9 |
20-08 | Probably not Wilson disease | 9/9 | |
MT-TL1 | 20-09 | No variant | 6/6 |
20-10 | No variant | 6/6 | |
MT-TK | 20-11 | m.8344A>G | 5/5 |
20-12 | No variant | 5/5 | |
GJB2 | 20-13 | c.35del, p.Gly12Valfs*2, heterozygote | 11/9 |
20-14 | No variant | 11/11 | |
LHON | 20-15 | m.3460G>A | 6/6 |
20-16 | No variant | 6/6 | |
RET | 20-17 | c.2753T>C, p.Met918Thr, heterozygote | 7/7 |
20-18 | No variant | 7/7 | |
SCA | 20-19 | Positive, SCA causing allele with full penetrance | 6/6 |
20-20 | Normal (no risk of SCA) | 6/6 | |
APOE genotype | 20-21 | APOE ε3/ε3 genotype | 47/47 |
20-22 | APOE ε2/ε3 genotype | 47/47 | |
Achondroplasia | 20-23 | FGFR3, G380R mutation, POSITIVE | 8/8 |
20-24 | FGFR3, G380R mutation, NEGATIVE | 8/8 | |
MTHFR genotype | 20-25 | MTHFR 677C/Theterozygous genotype | 14/14 |
20-26 | MTHFR 677C/Theterozygous genotype | 14/14 | |
PWS/AS | 20-27 | Angelman syndrome | 6/5 |
20-28 | Normal methylation pattern | 6/6 | |
DMD | 20-29 | Exon 49-52 deletion | 8/8 |
20-30 | No deletion/duplication | 8/8 | |
HD | 20-31 | Full penetrance | 5/5 |
20-32 | No risk of HD | 5/5 | |
FMR1 | 20-33 | Full mutation | 9/9 |
20-34 | No expansion | 9/9 | |
TGFBI | 20-35 | TGFBI, R124H mutation, NEGATIVE | 14/14 |
20-36 | TGFBI, R124H mutation, NEGATIVE | 14/14 | |
SBMA | 20-37 | Full penetrance | 4/4 |
20-38 | No risk of SBMA | 4/4 | |
SMA | 20-39 | SMN1, Exon7, homozygous deletion | 9/9 |
20-40 | Reduced probability of SMA | 9/9 | |
2020 2nd trials | |||
ABO genotype | 20-03 | O/O genotype | 16/16 |
20-04 | B/O genotype | 16/16 | |
BRCA1 | 20-41 | c.798_799del, p.Ser267Lysfs*19, heterozygote | 27/27 |
20-42 | No variant | 26/26 | |
BRCA2 | 20-43 | c.5946del, p.Ser1982Argfs*22, homozygote | 27/23 |
20-44 | No variant | 27/27 | |
TP53 | 20-45 | Ungraded | 8 |
20-46 | No variant | 8/8 | |
ATP7B | 20-47 | c.2930C>T, p.Thr977Met, heterozygote | 10/10 |
20-48 | Probably not Wilson disease | 10/10 | |
MT-TL1 | 20-49 | No variant | 6/6 |
20-50 | No variant | 6/6 | |
MT-TK | 20-51 | m.8344A>G | 5/5 |
20-52 | No variant | 5/5 | |
GJB2 | 20-53 | c.35del, p.Gly12Valfs*2, heterozygote(;)c.101T>C, p.Met34Thr, heterozygote | 12/11 |
20-54 | c.79G>A, p.Val27Ile, heterozygote | 12/10 | |
LHON | 20-55 | m.11778G>A | 6/6 |
20-56 | No variant | 6/6 | |
RET | 20-57 | c.1859G>T, p.Cys620Phe, heterozygote | 7/7 |
20-58 | No variant | 7/7 | |
SCA | 20-59 | Positive, SCA causing allele with full penetrance | 7/7 |
20-60 | Normal (no risk of SCA) | 7/7 | |
APOE genotype | 20-61 | APOE ε3/ε3 genotype | 49/49 |
20-62 | APOE ε3/ε3 genotype | 49/49 | |
Achondroplasia | 20-63 | FGFR3, G380R mutation, POSITIVE | 8/8 |
20-64 | FGFR3, G380R mutation, NEGATIVE | 8/8 | |
MTHFR genotype | 20-65 | MTHFR 677C/Theterozygous genotype | 15/15 |
20-66 | MTHFR 677C/Theterozygous genotype | 15/15 | |
PWS/AS | 20-67 | Prader-Willi syndrome | 7/7 |
20-68 | Normal methylation pattern | 7/7 | |
DMD | 20-69 | Exon 45 deletion | 8/8 |
20-70 | No deletion/duplication | 8/8 | |
HD | 20-71 | Full penetrance | 6/6 |
20-72 | No risk of HD | 6/6 | |
FMR1 | 20-73 | Premutation | 10/10 |
20-74 | No expansion | 10/10 | |
TGFBI | 20-75 | TGFBI, R124H mutation, NEGATIVE | 15/15 |
20-76 | TGFBI, R124H mutation, NEGATIVE | 15/15 | |
SBMA | 20-77 | Full penetrance | 5/5 |
20-78 | No risk of SBMA | 5/5 | |
SMA | 20-79 | SMN1, Exon7, homozygous deletion | 9/9 |
20-80 | Reduced probability of SMA | 9/9 | |
2021 1st trials | |||
ABO genotype | 21-01 | B/O genotype | 18/18 |
21-02 | B/O genotype | 18/18 | |
BRCA1 | 21-01 | c.4327C>G, p.Ser1436=, heterozygote(;)c.4308T>C, p.Arg1443Gly, heterozygote | 32/30 |
21-02 | c.4308T>C, p.Arg1443Gly, heterozygote | 32/30 | |
BRCA2 | 21-03 | c.6198_6199del, p.Ser2067Hisfs*10, heterozygote | 32/31 |
21-04 | No variant | 32/32 | |
TP53 | 21-05 | c.524G>A, p.Arg175His, heterozygote | 8/8 |
21-06 | No variant | 8/8 | |
ATP7B | 21-07 | c.3191A>C, p.Glu1064Ala, heterozygotec.3207C>A, p.His1069Gln, heterozygote | 10/10 |
21-08 | Probably not Wilson disease | 10/10 | |
MT-TL1 | 21-09 | No variant | 6/6 |
21-10 | No variant | 6/6 | |
MT-TK | 21-11 | m.8344A>G | 5/5 |
21-12 | No variant | 5/5 | |
GJB2 | 21-13 | c.176_191del, p.Gly59Alafs*18, heterozygote(;)c.235del, p.Leu79Cysfs*3, heterozygote | 9/9 |
21-14 | No variant | 9/9 | |
LHON | 21-15 | m.11778G>A | 7/7 |
21-16 | No variant | 7/7 | |
RET | 21-17 | c.1853G>C, p.Cys618Ser, heterozygote | 8/8 |
21-18 | No variant | 8/8 | |
SCA | 21-19 | Positive, SCA causing allele with full penetrance | 7/7 |
21-20 | Normal (no risk of SCA) | 7/7 | |
APOE genotype | 21-21 | APOE ε3/ε3 genotype | 50/50 |
21-22 | APOE ε3/ε3 genotype | 50/50 | |
Achondroplasia | 21-23 | FGFR3, G380R mutation, POSITIVE | 8/8 |
21-24 | FGFR3, G380R mutation, NEGATIVE | 8/8 | |
MTHFR genotype | 21-25 | MTHFR 677C/Theterozygous genotype | 14/14 |
21-26 | Homozygous normal (wild type/wild type) | 14/14 | |
PWS/AS | 21-27 | Angelman syndrome | 7/7 |
21-28 | Normal methylation pattern | 7/7 | |
DMD | 21-29 | Exon 46-50 deletion | 8/8 |
21-30 | No deletion/duplication | 8/8 | |
HD | 21-31 | Full penetrance | 6/6 |
21-32 | No risk of HD | 6/6 | |
FMR1 | 21-33 | Premutation | 10/10 |
21-34 | No expansion | 10/10 | |
TGFBI | 21-35 | TGFBI, R124H mutation, NEGATIVE | 15/15 |
21-36 | TGFBI, R124H mutation, NEGATIVE | 15/15 | |
SBMA | 21-37 | Full penetrance | 5/5 |
21-38 | No risk of SBMA | 5/5 | |
SMA | 21-39 | SMN1, Exon7, homozygous deletion | 9/9 |
21-40 | Reduced probability of SMA | 9/9 | |
2021 2nd trials | |||
ABO genotype | 21-03 | B/B genotype | 18/17 |
21-04 | O/O genotype | 18/16 | |
BRCA1 | 21-41 | c.5137del, p.Val1713*, heterozygote | 30/29 |
21-42 | No variant | 30/30 | |
BRCA2 | 21-43 | c.125A>G, p.Tyr42Cys, heterozygote | 30/29 |
21-44 | No variant | 30/30 | |
TP53 | 21-45 | c.652_654del, p.Val218del, homozygote | 8/8 |
21-46 | No variant | 8/8 | |
ATP7B | 21-47 | c.2930C>T, p.Thr977Met, heterozygote | 10/10 |
21-48 | Probably not Wilson disease | 10/10 | |
MT-TL1 | 21-49 | No variant | 6/6 |
21-50 | No variant | 6/6 | |
MT-TK | 21-51 | m.8344A>G | 5/5 |
21-52 | No variant | 5/5 | |
GJB2 | 21-53 | c.35del, p.Gly12Valfs*2, heterozygote(;)c.101T>C, p.Met34Thr, heterozygote | 8/8 |
21-54 | c.79G>A, p.Val27Ile, heterozygote | 8/7 | |
LHON | 21-55 | m.3460G>A | 7/7 |
21-56 | No variant | 7/7 | |
RET | 21-57 | c.2753T>C, p.Met918Thr, heterozygote | 8/8 |
21-58 | No variant | 8/8 | |
SCA | 21-59 | Positive, SCA causing allele with full penetrance | 7/7 |
21-60 | Normal (no risk of SCA) | 7/7 | |
APOE genotype | 21-61 | APOE ε3/ε3 genotype | 48/48 |
21-62 | APOE ε3/ε3 genotype | 48/48 | |
Achondroplasia | 21-63 | FGFR3, G380R mutation, POSITIVE | 8/8 |
21-64 | FGFR3, G380R mutation, NEGATIVE | 8/8 | |
MTHFR genotype | 21-65 | MTHFR 677C/Theterozygous genotype | 14/14 |
21-66 | MTHFR 677T/Thomozygous genotype | 14/13 | |
PWS/AS | 21-67 | Prader-Willi syndrome | 7/7 |
21-68 | Normal methylation pattern | 7/7 | |
DMD | 21-69 | Exon 4-43 deletion | 8/8 |
21-70 | No deletion/duplication | 8/8 | |
HD | 21-71 | Full penetrance | 6/6 |
21-72 | No risk of HD | 6/6 | |
FMR1 | 21-73 | No expansion | 10/10 |
21-74 | No expansion | 10/10 | |
TGFBI | 21-75 | TGFBI, R124H mutation, NEGATIVE | 15/15 |
21-76 | TGFBI, R124H mutation, NEGATIVE | 15/15 | |
SBMA | 21-77 | Full penetrance | 5/5 |
21-78 | No risk of SBMA | 5/5 | |
SMA | 21-79 | SMN1, Exon7, homozygous deletion | 8/8 |
21-80 | Reduced probability of SMA | 8/8 |
Abbreviations: S, specimen; T/A, total no. of participants/acceptable responses; MELAS, mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes; MERRF, myoclonic epilepsy with ragged red fibers; LHON, Leber hereditary optic neuropathy; RET, multiple endocrine neoplasia 2; SCA, spinocerebellar ataxia; APOE, apolipoprotein E; MTHFR, methylenetetrahydrofolate reductase; PWS/AS, Prader-Willi and Angelman syndrome; DMD, Duchenne muscular dystrophy; HD, Huntington’s disease; FMR1, fragile X messenger ribonucloprotein 1; TGFBI, transforming growth factor beta induced; SBMA, spinal and bulbar muscular atrophy; SMA, spinal muscular atrophy.
*Omit ‘GO’ or ‘GG’ from the specimen number.
신빙도조사에 참여한 기관 수는 검사항목에 따라 다소 차이가 있었으나, 2018년부터 2021년까지 전반적으로 증가하는 추세를 보였다. 2018년 1차부터 2021년 2차까지 유전질환 진단유전검사 신빙도조사에 참여한 기관의 수는 각각 연도별 회차별로 46, 47, 53, 51, 54, 56, 59, 57개 기관이었고, 각 기관의 참여종목 수는 한 종목부터 모든 종목까지 다양하였다. 기타 유전검사 신빙도조사에 참여한 기관의 연도별 회차별 수는 앞과 같은 순서로 각각 12, 12, 13, 14, 16, 16, 18, 18개 기관이었다.
유전질환 진단유전검사는 원인 유전변이의 종류 및 유전질환을 고려하여 다음과 같이 총 20종목으로 구성하였다: 유전자 내 다양한 위치의 염기변이에 의해 발생하고 진단을 위해 염기서열검사가 필요한 유전질환 8종목(
참여기관별로 검사에 사용한 검사법은 Table 2와 같았다. 검사법을 입력하지 않은 기관이 있어 검사종목별로 검사법의 비율을 계산하지 않았다. 유전자 내 다양한 위치의 염기변이에 의해 발생하는 질환의 경우, 대부분 염기서열검사를 자체검사법으로 사용하고 있었다. 특정 변이를 검출하기 위한 용도로 real-time PCR을 기반으로 하는 상용 시약이 증가하는 추세를 보였다.
Table 2 . Mutation detection methods used in the molecular diagnostics test survey in 2018–2021*.
Tests | Mutation detection methods | Response | |||||||
---|---|---|---|---|---|---|---|---|---|
2018 1st | 2018 2nd | 2019 1st | 2019 2nd | 2020 1st | 2020 2nd | 2021 1st | 2021 2nd | ||
ABO genotype | Allele-specific PCR | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Sanger sequencing | 9 | 9 | 11 | 11 | 13 | 13 | 15 | 15 | |
Single base extension (SNaPshot) | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | |
BRCA1 | Sanger sequencing | 19 | 19 | 22 | 23 | 25 | 27 | 32 | 30 |
BRCA2 | Sanger sequencing | 19 | 19 | 24 | 23 | 25 | 27 | 32 | 30 |
TP53 | Sanger sequencing | 6 | 3 | 7 | 6 | 8 | 8 | 8 | 8 |
ATP7B | Sanger sequencing | 8 | 1 | 7 | 6 | 9 | 9 | 10 | 10 |
Single base extension (SNaPshot) | 1 | ||||||||
MT-TL1 | Sanger sequencing | 6 | 2 | 6 | 4 | 6 | 6 | 6 | 6 |
MT-TK | Sanger sequencing | 5 | 1 | 5 | 3 | 5 | 5 | 5 | 5 |
GJB2 | Sanger sequencing | 11 | 5 | 10 | 8 | 9 | 10 | 8 | 8 |
Real-time PCR, melting curve analysis | 1 | 1 | 1 | 1 | |||||
Real-time PCR | 1 | 1 | |||||||
LHON | Sanger sequencing | 5 | 1 | 4 | 2 | 5 | 5 | 6 | 6 |
Single base extension (SNaPshot) | 1 | 0 | 1 | 1 | 1 | 1 | 1 | ||
RET | Sanger sequencing | 8 | 2 | 7 | 5 | 7 | 7 | 8 | 8 |
SCA | PCR and fluorescent based capillary electrophoresis (fragment length analysis) | 7 | 7 | 7 | 4 | 6 | 7 | 7 | 7 |
APOE genotype | Allele-specific PCR | 5 | 5 | 6 | 4 | 3 | 4 | 4 | 4 |
Line probe assay (LIPA) | 1 | ||||||||
PCR and gel electrophoresis | 1 | 1 | 1 | 1 | 2 | 2 | 1 | 1 | |
PCR (include multiplex), gel electrophoresis | 3 | 3 | 3 | 2 | 2 | 1 | 2 | 2 | |
Real-time PCR | 25 | 28 | 32 | 32 | 34 | 33 | 33 | 31 | |
Real-time PCR, hydrolysis probe | 1 | 1 | 1 | 2 | 3 | 3 | 3 | 3 | |
Real-time PCR, melting curve analysis | 1 | 1 | 1 | 1 | 1 | 4 | 5 | 6 | |
RFLP (restriction fragment length polymorphism) | 1 | 1 | |||||||
Sanger sequencing | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 1 | |
Achondroplasia | Sanger sequencing | 8 | 8 | 8 | 6 | 8 | 8 | 8 | 8 |
MTHFR genotype | Allele-specific PCR | 1 | 1 | 1 | 1 | 1 | |||
PCR and gel electrophoresis | 1 | 1 | 1 | 1 | 1 | 1 | |||
Real-time PCR | 2 | 1 | 3 | 3 | 3 | 3 | |||
Real-time PCR, hydrolysis probe | 2 | 2 | 3 | 3 | 2 | 2 | |||
Real-time PCR, melting curve analysis | 1 | 1 | 1 | 1 | 1 | 1 | |||
RFLP (restriction fragment length polymorphism) | 3 | 1 | 1 | 2 | 2 | 2 | |||
Sanger sequencing | 4 | 1 | 3 | 3 | 3 | 3 | 3 | ||
Single base extension (SNaPshot) | 1 | 1 | 1 | 1 | 1 | ||||
PWS/AS | PCR and gel electrophoresis, methylation specific | 4 | 2 | 3 | 3 | 3 | |||
MLPA, methylation specific | 1 | 1 | 3 | 3 | 4 | 4 | |||
MLPA | 1 | 1 | |||||||
DMD | MLPA | 6 | 3 | 8 | 8 | 8 | 8 | ||
HD | PCR and fluorescent based capillary electrophoresis (fragment length analysis) | 5 | 1 | 5 | 6 | 6 | 6 | ||
FMR1 | fragile X messenger ribonucleoprotein 1 | 7 | 4 | 5 | 6 | 8 | 8 | ||
Southern blot | 1 | ||||||||
Triplet repeat primed PCR and fluorescent based capillary electrophoresis | 3 | 1 | 4 | 4 | 2 | 2 | |||
TGFBI | Sanger sequencing | 11 | 9 | 8 | 5 | 8 | 7 | 8 | 7 |
SBMA | Real-time PCR | 3 | 4 | 4 | 4 | 5 | 5 | 5 | 5 |
Real-time PCR, hydrolysis probe | 1 | 3 | 3 | 4 | 1 | 3 | 2 | 3 | |
PCR and fluorescent based capillary electrophoresis (fragment length analysis) | 5 | 1 | 4 | 5 | 5 | 5 | |||
SMA | MLPA | 5 | 3 | 7 | 7 | 7 | 7 | ||
RFLP (restriction fragment length polymorphism) | 2 | 0 | 2 | 1 | 1 | 1 | |||
MLPA, methylation specific | 1 | 1 |
Abbreviations: PCR, polymerase chain reaction; RET, multiple endocrine neoplasia 2; HD, Huntington’s disease; SCA, spinocerebellar ataxia; SBMA, spinal and bulbar muscular atrophy; LHON, Leber hereditary optic neuropathy; MELAS, mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes; MERRF, myoclonic epilepsy with ragged red fibers; PWS/AS, Prader-Willi and Angelman syndrome; DMD, Duchenne muscular dystrophy; MLPA, multiple ligation probe amplification; SMA, spinal muscular atrophy; APOE, apolipoprotein E; MTHFR, methylenetetrahydrofolate reductase; FMR1, fragile X messenger ribonucleoprotein 1.
*Omit no responses.
신빙도조사에서 unacceptable 결과를 보인 주요 사례는 아래와 같았다.
SCA 분자유전자검사에서 예상결과와 불일치했던 1예로 2018년 1차의 경우, 해당 기관은 SCA2만 검사하는 기관이었다. 따라서 SCA7 염기 반복구조 증폭을 검출하지 못해 no risk for SCA로 잘못 보고 하였다.
FMR1 분자진단검사에서는 성별을 반대로 보고한 기관이 2018년도 2차에 1개, 2019년도 1차에 2개였다. 2018년도 1차에서는 다른 기관들은 모두 full mutation으로 해석하였으나, 이와 달리 premutation으로 보고한 기관이 1개였다.
DMD 분자진단검사는 2018년 2차의 GG-18-69와 GG-18-70의 결과를 반대로 입력한 1예 외엔 매 회차 모든 기관에서 예상결과와 일치하는 결과를 보고하였다.
매 회차 각 종목에 참여한 모든 기관의 수의 합과 acceptable response를 보인 모든 기관의 수의 합을 이용한 정답률은 2018년 1차부터 2021년 2차까지 순서대로 98.43%, 99.31%, 92.16%, 99.51%, 98.58%, 98.64%, 99.08%, 98.68%였다.
Unacceptable 결과의 종류와 추정되는 원인, 각각에 해당되는 예의 수를 정리한 표는 Table 3과 같다.
Table 3 . Categories of incorrect answers.
Scenario | No. of cases |
---|---|
Report variants that don’t exist | 1 |
Fail to report variants | 23 |
Report variants that is outside of testing regions | 9 |
Report wrong zygosity of variants | 7 |
Clerical error | 4 |
Wrong test sample | 1 |
Nucleotide number typo | 2 |
Wrong gene name | 1 |
Incorrect interpretation of variants | 21 |
Fail to search previously reported cases of variants | 1 |
Misinterpreting pathogenicity of variants | 17 |
Misidentify patients' gender | 3 |
기타 진단유전검사 ABO 유전형 검사에서 2019년 1차에 1기관, 2021년 2차에 2기관이 각각 1항목, 2항목에 불일치한 결과를 보고하였다.
2018–2021년도 진단유전검사 신빙도조사의 경우, 2019년 1차 1회를 제외하고 정답률 98%를 상회하는 우수한 결과를 보였다. 하지만 일부 검사 및 보고단계에서 다음과 같은 사항에 대해 주의 및 개선이 필요할 것으로 판단되었다.
염기서열변이 기술 시 Human Genome Variation Society (HGVS)의 최신 표준권고안을 참고하도록 안내하고, 또한 triple-letter amino acid code를 사용하도록 권장하였으나, 각 기관마다 nucleotide level과 protein level의 다양한 변이 기술방법을 보여주었다. 유전질환에 대한 이해와 유전진단 기술이 발전하면서 HGVS 권고안 역시 계속 개정되므로 항상 최신의 권고안을 숙지할 수 있도록 기관 내 교육이 필요할 것으로 보인다[1,2].
단순 오타나 잘못된 검체번호에 결과를 입력하는 등 사무적 오류로 인한 부적합 결과가 반복적으로 관찰되었다. 잘못된 검체번호에 결과를 입력한 경우는 최종 입력과정이 아니라 검체 접수과정, 즉 환자-검체 일치과정부터 잘못되었을 수 있다. 따라서 접수에서 최종 보고에 이르기까지 다양한 단계에서 발생할 수 있는 사무적 오류를 적시에 확인하고 수정할 수 있도록 체계를 구축할 필요가 있다.
마지막으로 일부 기관의 경우 제시된 reference transcript와 상이한 자체 reference transcript를 사용함으로써, 다른 참여기관과 다른 결과를 보고하는 경우가 있었다. 매회 신빙도조사 안내문에 각 검사항목의 reference transcript 및 주의사항을 제시하고 있으므로, 반드시 이를 확인하는 과정이 필요할 것으로 보인다[3].
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