PHWR Public Health Weekly Report

Rare diseases refer to those with a prevalence of less than 20,000 of the total population in Republic of Korea (ROK). Although each disease is extremely rare, the total number of rare diseases accounts for 5–10% of ROK’s total population. There are around 7,000 rare diseases, with approximately 80% known to be caused by genetics [1]. Genetic diseases due to mutations in specific genes can be diagnosed by checking the gene sequence. The current diagnostic process implemented for genetic diseases involves determining the causative gene and searching for mutations in the corresponding genes. With the completion of the Human Genome Project, the sequence of the human genome has been completely clarified, thereby accelerating the diagnosis of inherited rare diseases. Genome sequencing methods have also evolved from Sanger sequencing to next generation sequencing (NGS), which has led to a more active diagnosis of rare genetic diseases [2].

Sanger sequencing, which was introduced in the 1970s and considered a representative technique in medical genetic diagnosis until the early 2000s, is a method of sequencing exons of less than 1 kb and is suitable for sequencing single genes. However, there are limitations in that the method is expensive and requires significant effort to sequence inherited diseases involving multiple or large genes.

NGS, also known as massive parallel sequencing, is a method that can sequence a large number of bases at once, which overcomes the limitations of Sanger sequencing, enabling the sequencing of diseases with multiple related genes and large genes with a large number of exons [3].

While NGS has enabled rapid gene sequencing, a large number of variants are identified, posing challenges in the analysis of such variants.

It is necessary to predict the possible etiology by determining whether mutations in unreported genes cause abnormalities in gene products. Therefore, determining the diagnosis and follow-up management of the test subjects and predicting the etiology of the discovered gene mutation have become an integral part of the genetic testing process.

Genetic testing using NGS is actively conducted for diagnostic testing and research purposes. However, it has not yet expanded to the clinical practice in the field of medical genetics. There is a shortage of experts who can interpret variant of unknown significance (VUS) discovered through NGS, especially those with unclear etiology.

Incorrect interpretation of the results after genetic testing or misdiagnosis due to misunderstanding of the results has become an issue in clinical practice [4].

To solve these problems, we introduced a system that interprets the results after genetic testing by experts and provides genetic counseling according to the interpretation to help diagnose, treat, and manage patients with rare genetic diseases.

This study, focusing on tertiary general hospitals, was conducted from March 2022 to June 2023 for patients with rare genetic diseases and their families. It supported the interpretation of the results and the direction of treatment after the target gene panel test, whole exome sequencing, and whole genome sequencing by NGS.

If diagnosis interpretation support is required, the request form for the interpretation of results that includes information, such as the reason for the referral, the referring hospital, the doctor in charge, the referral department, phone number, e-mail, patient name, date of birth, sex, race, genetic test results, major clinical symptoms, other test results, and family history, was filled out and referred to the Korea Disease Control and Prevention Agency’s Integrated Disease and Health Management System or sent by e-mail. Consent to collecting and using the patient’s personal information and provision to a third party was submitted together.

Medical genetic experts, such as certified MD medical geneticist and PhD medical geneticist, provided the initial written interpretation and follow-up measures. Additionally, genetic counseling was provided by a certified clinical genetics physician and certified genetic counselors to help with diagnosis and follow-up management.

Certified MD medical geneticists are specialists who can handle complex medical procedures, such as patient diagnosis, examination, treatment direction, deciding prognosis, and genetic counseling for family members. PhD medical geneticists are doctoral-level professionals who can advise clinicians on patients with an understanding of all complex fields of clinical genetics and with the ability to analyze and interpret complex clinical genetics in cooperation with certified MD medical geneticists. They are certified by the Korean Society of Medical Genetics [5].

Fifteen referrals for interpreting results were requested through the result interpretation support system, and the results were interpreted through multidisciplinary consideration (Table 1).

Table 1 Interpretation of genetic test results and the content and time required for genetic counseling

No.	Disease	Results of genetic testing	Interpretation of the results	Supports for genetic counseling
				Subject	Counseling details	Time (min)
						Serve/prepare
1	Ehlers Danlos syndrome	Ehlers Danlos panel: negative. FBN1 sequencing: negative. MLPA: negative. GLA: negative. WGS: negative.	Possibility of hypermobile type EDS for which the causative gee has not been identified	Patient	MHHear, PWrite, EDU, DESCR, CHEKU, CONSUL, ADD, PSYC, ANSW, FOLLOW, description of risk assessment and family testing, guidance on collaboration with various departments for treatment and management	40/90
2	Congenital muscular dystrophy	LMNA: c.745C>T (p.R249W) heterozygous LP variant. Mitochondrial gene: negative. WGS: No significant changes other than LMNA variant.	As compared to the clinical picture of the test subject, it can be diagnosed as muscular dystrophy or congenita caused by a mutation in the LMNA gene	-	-	-
3	r/o Syndromic disorder, r/o Noonan syndrome	Karyotype: 46,XY. CMA: negative. WGS: negative.	It is recommended to check whether additional phenotypes appear in the test subject, and to determine whether genetic evaluation is necessary	-	-	-
4	Hemophagocytic lymphohistiocytosis	Karyotype: 46,XY. NGS panel test for immunodeficiency: 3 VUS. WGS: SV in STAT5B and STAT5A.	The three mutations in the immunodeficiency gene panel do not correspond to the test subject’s disease, and the SV mutation in STAT5A/STAT5B is considered the causative mutation. Carrier testing of parents for SV mutations is recommended.	Father of patient	MHHear, PWrite, EDU, DESCR, CHEKU, CONSUL, ADD, PSYC, ANSW, FOLLOW	40/60
5	Autism spectrum disorder	Karyotype: 46,XX. CMA: arr[GRCh37] 12q23.3q24.13 (106,044,030_ 114,026,006)x2 hmz. WGS: SV in ITGAM.	Only one heterozygote was identified in the recessively inherited ITGAM gene, and a possibility of a new gene related to autism, so carrier testing is recommended for parents	Mother of patient	MHHear, PWrite, EDU, DESCR, PSYC, ANSW, FOLLOW, consultation on chromosomal microarray test results and explanation of additional genetic testing	60/60
6	RP	RP panel: heterozygote LP in ABCA4 and PDE6A	Each of one heterozygous LP mutation was observed in each of the two recessively inherited genes associated with the disease, and additional tests such as WGS and MLPA were recommended to confirm the remaining mutations	Patient	MHHear, PWrite, EDU, DESCR, CONSUL, ADD, FAMILY, PSYC, ANSW, FOLLOW	50/60
7	VLCAD	Expired fetus: fatty acid-related ACADVL1 gene–homozygous c.996dup. And heterozygous c.852_856del in SLC25A1 gene were detected. Homozygous LP in ACADVL1 and heterozygous PV in SCL25A13.	Expired fetus was diagnosed with VLCAD, and carrier testing of the parents confirmed that each was a heterozygous mutation carrier. The clinical symptoms of the expired fetus are correlated with the SLC25A13 gene mutation, so additional testing is recommended to confirm the remaining mutations.	Mother of fetus	MHHear, PWrite, EDU, DESCR, CONSUL, PSYC, ANSW, FOLLOW, provision of information on registration to special exempted calculation health insurance and medical expense support, explain of prenatal diagnosis	60/60
8	Leigh disease	RP panel: RIMS1 VSU. WGS: PV in MT-ATP6.	The patient’s ocular symptoms are similar to those of RIMS1, but the developmental delay, motor delay, and ataxia cannot be explained. m.8783G>A in the mitochondrial gene is a mutation reported in Leigh encephalopathy, and this corresponds to the clinical picture of the test subject, leading to the diagnosis of Leigh disease due to the m.8983G>A mutation. Recommendation of clinical evaluation of maternal ancestry of the patient.	Mother of patient	MHHear, PWrite, EDU, DESCR, CHEKU, CONSUL, ADD, FANILY, PSYC, ASNW, FOLLOW, provision of information on registration to special exempted calculation health insurance and medical expense support, explanation of collaboration with other departments for treatment and management	40/60
9	Ehlers Danlos syndrome	COL5A1/COL5A2 sequencing: negative. WGS: c.1977G>A (p.P659=) PV in COL5A2.	The initial test was negative, but upon re-test results and reinterpretation of the previous test, c.1977G>A, which was considered a benign, was interpreted as PV causing splicing abnormality and diagnosed as EDS classic type 2	Mother of patient	MHHear, PWrite, EDU, DESCR, CHEKU, CONSUL, ADD, FAMILY, PSYC, ASNW, FOLLOW, provision of information on registration to special exempted calculation health insurance and medical expense support, explanation of collaboration with other departments for treatment and management	60/60
10	r/o Leiomyomatosis and renal cell cancer	FH sequencing: c.842C>T (p.T28I) VUS in FH. WES: FH c.842C>T (p.T28I) was analyzed as LP.	FH gene is a related to leiomyomatosis renal cell cancer and matches the patient’s clinical picture. Recommendation of carrier testing for family members.	Patient	MHHear, PWrite, EDU, DESCR, CONSUL, ADD, FAMILY, PSYC, ANSW, FOLLOW	60/90
11	Osteogenesis imperfecta	COL1A1/COL1A2 and RUNX2 sequencing: negative. WGS: negative. In WGS re-analysis, exon34-52 deletion was suspected in COL1A2. Additional confirm with MLPA.	Since COL1A2 exon34-51 deletion was not a point mutation, it was difficult to confirm through sequencing, and the deletion was confirmed using the MLPA	Patient	MHHear, PWrite, EDU, DESCR, CHEKU, CONSUL, PSYC, ANSW, FOLLOW, prenatal diagnosis is possible when planning to have children in the future, and prenatal diagnosis is explained	40/60
12	Usher syndrome	In the RP panel, two LP in USH2A c.2802T>G (p.C934W) and c.15017C>T (p.T5006M) were detected	Diagnosed as Usher syndrome type 2 and recommend family testing	Patient	MHHear, PWrite, EDU, DESCR, CONSUL, PSYC, ANSW, FOLLOW, recommend family testing after risk assessment	60/60
13	Neurofibromatosis type 1	In NF1 sequencing, c.4930G>C (p.D1644H) VUS was detected	A family member with the same symptoms showed the same mutation, and through reinterpretation and LP analysis, was diagnosed as NF1 due to the c.4930G>C (p.D1644H) mutation	Patient	MHHear, PWrite, EDU, DESCR, CHEKU, CONSUL, FAMILY, PSYC, ANSW, FOLLOW, provision of information on registration to special exempted calculation health insurance and medical expense support	40/60
14	RP	In RP pane, heterozygote LP, c.6181del (p.I2061fs) in RP1 was detected	The RP1 gene is a recessively inherited gene, so confirmation of the remaining mutations is required. Recommendation of additional testing to determine whether Alu insertion mutation in the RP1 gene, which is relatively common in Korea, is present.	Patient	MHHear, PWrite, EDU, DESCR, CONSUL, ADD, FAMILY, PSYC, ANSW, FOLLOW	40/60
15	r/o Intellectual developmental disorder	In WES, c.271C>T (p.R91C) VUS in PPP2R5D was detected	The clinical picture of the test subject is consistent with the PPP2R5D genetic disease, but analysis is difficult due to insufficient information. To confirm whether the above mutation was de novo, parents were recommended to be tested as carriers, and additional tests such as CMA were recommended to confirm SVs that could not be confirmed through WES.	Mother of patient	MHHear, PWrite, EDU, DESCR, CONSUL, ADD, PSYC, ANSW, FOLLOW, explaining the need for parental testing	60/60

MLPA=muliplex ligation-dependent probe amplification; WGS=whole genome sequencing; EDS=Ehlers Danlos syndrome; CMA= chromosomal microarray; VUS=variant of unknown significance; SV=structural variant; RP=retinitis pigmentosa; LP=likely pathogenic; PV=pathogenic variant; VLCAD=very long chain acyl-CoA dehydrogenase; WES=whole exome sequencing; MHHear=medical history hearing; PWrite=pedigree writing; EDU=genetics education and explanation of inheritance modes; DESCR=description of the diseases; CHEKU=explain the importance of regular checkups and management; CONSUL=consultation on result of genetic testing; ADD=explain of additional genetic testing; FAMILY=explain the need for family testing based on result of genetic testing; PSYC=psychosocial counseling and support; ANSW=answers to their inquiries; FOLLOW= follow-up..

For these 15 cases, we analyzed mutations in 14 genes for 12 types of diseases. It included two negative results, six likely pathogenic variants (LPVs), three pathogenic variants (PVs), two structural variants (SV), and two VUS.

Based on the reinterpretation of the results, we arrived at a reasonable diagnosis, provided guidance for subsequent reanalysis and further testing, and provided appropriate genetic counseling for 13 cases.

Genetic counseling was conducted for 40 to 90 minutes for each patient and included taking a medical history, making a family tree, genetic education and explanation of genetic methods, explanation of diseases, consultation on genetic test results, psychological counseling and support, answers to questions, and follow-ups.

Despite the development of genetic testing techniques, patients often go through the diagnostic odyssey, which refers to the journey of traveling from one medical institution to another for a long period to get diagnosed with rare genetic diseases. Even after genetic testing is performed, there are cases where the diagnosis is incorrect or delayed due to the difficulty in interpretation [4].

Due to the rarity of genetic diseases, information about diseases is limited, making it difficult for medical personnel to interpret the diagnosis results, provide treatment, and manage patients. It is important for clinical geneticists and bioinformaticians to identify the patients’ clinical symptoms and the gene mutations that cause the disease among various mutations; however, the number of them is lacking. It is necessary to improve the access to medical care that interprets the testing results and provide tailored services for rare genetic diseases to patients and medical professionals.

Once diagnosed, patients and their family members can receive support, such as follow-up treatment, additional tests for family members, disease information, information about treatment and prognosis, psychosocial support, and risk assessment for future pregnancies. Thus, obtaining a diagnosis as quickly as possible is very important for patients and their family members.

Rare genetic diseases require long-term treatment and management throughout life, and the economic burden not only on the patient, but also on the family and society, is great. Due to the patient’s need for various care, such as treatment, care, rehabilitation, special education, and social stigma, the quality of life is low. In several cases, there are only a few therapeutic drugs. It is reported that 5% of rare diseases have therapeutic drugs; however, most of them are imports, and even if they can be purchased in ROK, they are often not reimbursed. In addition, more than 80% of rare diseases are genetic diseases, which can recur or may be inherited within families and may result in weakened family function or family dissolution due to the psychological burden and stress. It is more important to provide tailored services to patients and their families, including not only diagnosis, but also treatment and management and social and psychological support. Providing professional genetic counseling services to patients and their families is essential.

Looking at examples from foreign countries where genetic counseling is commonly provided, the United States and Europe have cultivated genetic counselors through master’s programs since the early 1970s, providing genetic counseling services as part of the medical team. In Asia, genetic counselors have teamed up with clinical geneticists to provide genetic counseling services in Japan, Taiwan, Malaysia, Hong Kong, and Singapore since the early 2000s. However, in ROK, genetic counselors are not managed nationally yet [6,,-9].

The genetic test interpretation support project was implemented to shorten the time to get diagnosed, and it was of great help in the diagnosis and follow-up management by providing professional genetic counseling with certified genetic counselors and interpretation of results.

This study suggests that a team system approach in medical treatment, testing, and genetic counseling is organically provided and is an efficient method not only for patients with genetic diseases and their family members, but also for medical personnel for appropriate testing and its interpretation, management after diagnosis, and genetic counseling for rare genetic diseases. In the future, it is necessary that national level of recognition and support for genetic counseling professionals who can be in charge of efficient communicator in organized team system for results interpretation and create a new fee for genetic counseling. For this, systematic management is needed to standardize genetic counseling services.

Ethics Statement: This study was approved by the Institutional Review Board of the Asan Medical Center in Seoul to ensure ethical protection of the subjects (IRB number 2022-1406).

Funding Source: This study was supported by a research fund from the Korea Disease Control and Prevention Agency (no. 2022-11-022).

Acknowledgments: None.

Conflict of Interest: The authors have no conflicts of interest to declare.

Author Contributions: Conceptualization: IHC, BHL, JWL. Data curation: IHC, BHL, JWL. Formal analysis: GHK, IHC, BHL, JWL. Funding acquisition: BHL, JWL. Investigation: GHK, IHC, BHL. Methodology: IHC, BHL, JWL. Project administration: IHC, BHL, JWL. Resources: IHC, BHL. Supervision: GHK, IHC, BHL, JWL. Validation: IHC, BHL, JWL. Visualization: IHC, BHL, JWL. Writing – original draft: GHK, IHC. Writing – review & editing: GHK, IHC, BHL, JWL.