Standards for the interpretation of constitutional copy number gain: Recommendation from the American College of Medical Genetics and Genomics (ACMG) and Clinical Genome Resource (ClinGen) / 中华医学遗传学杂志

Copy number variants (CNVs) are common causes of human genetic diseases. CNVs detection has become a routine component of genetic testing, especially for pediatric neurodevelopmental disorders, multiple congenital abnormalities, prenatal evaluation of fetuses with structural anomalies detected by ultrasound. Although the technologies for CNVs detection are continuously improving, the interpretation is still challenging, with significant discordance across different laboratories. In 2020, the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen) developed a guideline for the interpreting and reporting of constitutional copy number variants, which introduced a quantitative, evidence-based scoring framework. Here, we detailed the key points of interpreting the copy number gain based on the guideline, used six examples of different categories to illuminate the scoring process and principles. We encourage a professional understanding and application of this guideline for the detected copy number gains in China in order to further improve the clinical evaluation accuracy and consistency across different laboratories.

Experience and lessons on guiding and governing clinical applications of chromosome microarray analysis in the United States / 中华医学遗传学杂志

Chromosome microarray analysis (CMA) has become the first-tier testing for chromosomal abnormalities and copy number variations (CNV). This review described the clinical validation of CMA, the development and updating of technical standards and guidelines and their diagnostic impacts. The main focuses were on the development and updating of expert consensus, practice resources, and a series of technical standards and guidelines through systematic review of case series with CMA application in the literature. Expert consensus and practice resource supported the use of CMA as the first-tier testing for detecting chromosomal abnormalities and CNV in developmental and intellectual disabilities, multiple congenital anomalies and autism. The standards and guidelines have been applied to pre- and postnatal testing for constitutional CNV and tumor testing for acquired CNV. CMA has significantly improved the diagnostic yields but still needs to overcome its technical limitations and face challenges of new technologies. Guiding and governing CMA through expert consensus, practice resource, standards and guidelines in the United States has provided effective and safe diagnostic services to patients and their families, reliable diagnosis on related genetic diseases for clinical database and basic research, and references for clinical translation of new technologies.

Clinical manifestation and gene analysis of a family with pseudoachondroplasia / 中华实用儿科临床杂志

Clinical manifestations and genes of a case from a family with pseudoachondroplasia caused by COMP gene mutation treated in the Department of Pediatrics of the First People′s Hospital of Yunnan Province were retrospectively analyzed.The male patient aged 3 years and 3 months old had a history of slow growth for 1 year.Physical examinations showed that the patient′s height: 87.5 cm (less than -3 SD), 55.0 cm on top, 32.5 cm on bottom, mild O-leg, Nervous system physical examination suggested normal muscle strength of lower limbs and low muscle tone.Genetic examination revealed that the heterozygous gene variation of exon 11 of the COMP gene was chr19: 18897437 A >g [hg19], nm_000095.2, c.1159T >c, p.CY3 387 Arg, namely the transformation of cysteine to arginine at position 1159 of the translation product protein.Genetic testing is an important basis for the diagnosis of pseudoachondroplasia.It can avoid mistreatment, so as not to affect the predicted adult height of children.

Genetic analysis of three children with disorders of sex development caused by structural rearrangements of Y chromosome / 中华医学遗传学杂志

OBJECTIVE@#To explore the genetic basis of three children with disorders of sex development (DSD) in association with rare Y chromosome rearrangements.@*METHODS@#The three children, who all featured short stature and DSD, were subjected to G banding chromosomal karyotyping, multiplex PCR for Y chromosomal microdeletion, sequencing of the whole SRY gene, SNP-array analysis for genomic copy number variations, and fluorescence in situ hybridization (FISH).@*RESULTS@#The combined analysis revealed chromosomal abnormalities in all of the three children, including 46,X,t(X;Y)(p22.3;q11.2) in case 1, mos 45,X,der(7)pus dic(Y:7)(p11.3p22)del(7)(p21.2p21.3) del(7)(p12.3p14.3) [56]/45,X [44] in case 2, and mos 45,X [50]/46,X,idic(Y)(q11.22) [42]/47,X,idem×2 [4]/47,XYY [2] in case 3.@*CONCLUSION@#Combined use of genetic techniques can delineate complex rearrangements involving Y chromosome in patients featuring short stature and DSD. Above findings have enabled molecular diagnosis and genetic counseling for the patients.

Wiedemann-Steiner syndrome caused by novel mutation of KMT2A gene: one case report and literature review / 中华内分泌代谢杂志

Objective To analyze the clinical and biochemical,as well as genetic characteristics of a patient with Wiedemann-Steiner syndrome (WDSTS).Methods The clinical data of a patient with WDSTS were collected.The patient was treated with recombinant human growth hormone (rhGH) combined with gonadotrophine-releasing hormone agonist (GnRHa).Blood samples of the patient and her parents were taken for whole-Exome Sequencing (WES).Relevant literatures about KMT2A mutations were reviewed.Results The 5-year old girl presented with growth retardation,with height 100 cm (-2.4 SD),torpid reaction,and facial anomalies including low hairline,thick eyebrow and hair,hypertelorism,a wide nasal bridge.She had small and puffy hands and feet,excessive hair around back of neck,bilateral forearm and lower limbs.Her GH peak level was 26.6 ng/ml during GH stimulation test.She was re-examined at the age of 10.4 years,with severe short stature (120 cm/-3.58 SD) and a Tanner stage 2 of breast development.Her bone age was found to be approximately 11.4 years.Height increased from 120 cm at the age of 10.4 years to 147.3 cm after rhGH treatment combined with GnRHa for 2.5 years.rhGH therapy alone continued for 1.1 years and a height of 150 cm was reached at the age of 14.9 years,with bone age 14 years.Gene sequencing revealed a de novo frameshift mutation (c.10051 delA,p.Thr3351 Leufs * 17) of exon 27 in KMT2A gene of the patient,but without any mutation in her parents.Through a literature review,seventy-one patients with WDSTS (including present case) presented with intellectual disability (70/71),facial anomalies (70/71),short stature (50/71),and hypertrichosis (39/71).Conclusion Patients presented with short stature,typical facial dysmorphism,intellectual disability,and hypertrichosis should be considered for WDSTS.The mutation p.Thr3351Leufs * 17 in the KMT2A gene detected in our patient is a novel mutation.This is so far the first report of WDSTS patient who was successfully treated with a combination of GH and GnRHa at the onset of puberty to improve her adult height.

Analysis of four carnitine-acylcarnitine translocase deficiency cases caused by homozygous mutation of SLC25A20 c.199-10T> G / 中华儿科杂志

Objective@#To investigate the clinical, biochemical and genetic features of four carnitine-acylcarnitine translocase deficiency cases.@*Methods@#Four cases diagnosed with carnitine-acylcarnitine translocase deficiency from Guangxi Maternal and Child Health Hospital were studied. DNA was extracted from dry blood filter for gene analysis. SLC25A20 gene analysis was performed in 1 case and the whole exon sequence analysis was performed in 3 cases.@*Results@#Retrospective study on unrelated carnitine-acylcarnitine translocase deficiency patients, the age of onset was 1-28 d, the age of death were 1.5-30 d, main clinical features were hypoglycemia (4 cases), arrhythmia (2 cases), sudden death (2 cases). Biochemical test showed hypoglycemia (1.2-2.0 mmol/L) , elevated creatine kinase (955-8 361 U/L) and creatine kinase isozyme(199-360 U/L), normal or decreased free carnitine level (3.70-27.07 μmol/L) , elevated long-chain acylcarnitine (palmityl carnitine 1.85-14.84 μmol/L). The gene tests showed that all 4 cases carried SLC25A20 gene c.199-10T> G homozygous mutation, inherited from their parents. By analyzing the haplotype, we found that the mutation loci of C. 199-10T> G were all in the same haplotype.@*Conclusion@#The c.199-10T> G mutation is an important molecular cause of carnitine-acylcarnitine translocase deficiency, which has relatively high frequency in Guangxi population, and is related to the founder effect.

Clinical and molecular analysis of two Chinese siblings with Bloom syndrome / 中华儿科杂志

Objective@#To expand the knowledge of the clinical and molecular characteristics of the children with Bloom syndrome.@*Methods@#Clinical data of two siblings with classic Bloom syndrome of Shanghai Children's Medical Center from January 2009 to June 2017 were obtained and analyzed. The DNA of peripheral blood was collected from two Bloom syndrome siblings and their parents during 2015. The mutations were detected with high-throughput sequencing by Illumina sequencing platform.@*Results@#The two siblings (probands) visited our department for short stature and growth retardation, they had full-term normal delivery after normal pregnancy of their mother. Both cases presented with feeding difficulties, malnutrition, microcephaly and mental retardation, repeated infection, symmetrical short stature and special faces. At first, the proband was an 8-year-3-month old girl, her height was 99.7 cm, body mass index (BMI) 12.07 kg/m2, head circumference was 45.5 cm, and birth weight was 1.6 kg. Her younger brother was 3-year-11-month old, his height was 86.6 cm, BMI was 14 kg/m2, birth weight was 1.95 kg, and the head circumference reached 36 cm at 16 months. No evidence of cancer and characteristic rash was detected at 8-year follow-up. Pathogenic complex heterozygous mutations c.772_773delCT, p.Leu258Glufs*7 and c.959+ 2T>A in BLM gene were detected in both siblings, which were separately inherited from their unaffected parents. Besides , c.959 + 2T>A has not been reported previously.@*Conclusions@#Children with Bloom syndrome are characterized by short stature, microcephaly, special faces, feeding difficulties, and immunodeficiency. And butterfly erythematous rash may be absent. The c.959+2T>A mutation detected in our patients maybe a novel pathogenic mutation.

Genetic analysis of two children patients affected with CHARGE syndrome / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To analyze two Chinese pediatric patients with multiple malformations and growth and development delay.</p><p><b>METHODS</b>Both patients were subjected to targeted gene sequencing, and the results were analyzed with Ingenuity Variant Analysis software. Suspected pathogenic variations were verified by Sanger sequencing.</p><p><b>RESULTS</b>High-throughput sequencing showed that both patients have carried heterozygous variants of the CHD7 gene. Patient 1 carried a nonsense mutation in exon 36 (c.7957C>T, p.Arg2653*), while patient 2 carried a nonsense mutation of exon 2 (c.718C>T, p.Gln240*). Sanger sequencing confirmed the above mutations in both patients, while their parents were of wild-type for the corresponding sites, indicating that the two mutations have happened de novo.</p><p><b>CONCLUSION</b>Two patients were diagnosed with CHARGE syndrome by high-throughput sequencing.</p>

Discussion on the standard of clinical genetic testing report and the consensus of gene testing industry / 中华医学遗传学杂志

The widespread application of next generation sequencing (NGS) in clinical settings has enabled testing, diagnosis, treatment and prevention of genetic diseases. However, many issues have arisen in the meanwhile. One of the most pressing issues is the lack of standards for reporting genetic test results across different service providers. The First Forum on Standards and Specifications for Clinical Genetic Testing was held to address the issue in Shenzhen, China, on October 28, 2017. Participants, including geneticists, clinicians, and representatives of genetic testing service providers, discussed problems of clinical genetic testing services across in China and shared opinions on principles, challenges, and standards for reporting clinical genetic test results. Here we summarize expert opinions presented at the seminar and report the consensus, which will serve as a basis for the development of standards and guidelines for reporting of clinical genetic testing results, in order to promote the standardization and regulation of genetic testing services in China.

The Clinical Experience of Integrated Traditional Chinese and Western Medicine in Treating Elderly Acute Myeloid Leukemia of SHEN Yiping / 浙江中医药大学学报

[Objective] To summarize Dr. SHEN Yiping's clinical experience of integrated traditional Chinese and western medicine in treating elderly acute myeloid leukemia (AML). [Methods]By examining with cases of illness and warding round,collecting the medical records of elderly AML patients treated by Dr. SHEN, learning the latest diagnosis and treatment guidelines, reading a large number of related papers and a large number of classical books, from the aspects of etiology and pathogenesis, therapeutic principles and methods, the clinical experience of the treatment of elderly AML were analyzed and summarized, and one medical record was provided.[Results]Dr. SHEN believes that the pathogenesis is deficiency syndrome accompanied with excess syndrome. Mostly due to congenital deficiency and poor basic functions, deficiency of spleen and kidney, heat poison intrusion, burning Jin as sputum, forcing blood going in wrong line, phlegm and blood stasis, evil accumulating in bone marrow and then suffered. Dr. SHEN uses heat-clearing, detoxifying and anti-cancer drugs to suppress and eliminate leukemia cells on the basis of chemotherapy and supplements beneficial drugs to achieve the goal of chemotherapy without harming the positive effect, he uses "Kangbai Yannian Tang" combined with decitabine and chemotherapy as a basic solution and changes flexibly by according to the clinical manifestations, changes of syndrome types of the patients, the clinical effect is remarkable, and the case had good results. [Conclusion]Dr. SHEN is good at integrated traditional Chinese and western, combining of syndrome differentiation and disease differentiation, using the combination of heat-clearing method and complement in the treatment of elderly AML, the experience and wonderful methods are worth learning and spreading.

The analysis of clinical manifestations and genetic mutations in a child with hereditary fructose intolerance / 临床儿科杂志

Objective To analysis the clinical and gene mutation characteristics of hereditary fructose intolerance (HFI). Methods The clinical features and the results of gene testing in the child with HFI and her parents were analyzed retrospectively. Gene sequencing was carried out by high-throughput sequencing and validated by Sanger sequencing. Results The 4-year-3-month old girl had recurrent hypoglycemia episodes and growth retardation. When the condition was stable, the levels of lactic acid and urine micro protein were slightly higher, and the levels of thyroid hormone, cortisol, glycosylated hemoglobin, insulin and C peptide were normal.EEG showed epileptiform activity.Gene sequencing revealed the presence of aldolase B gene(ALDOB) compound heterozygous mutations, a novel splicing mutations (c.325-1G>A) in intron 3 and a frameshift mutation (c. 865delC;p.L289fs*10) in exon 8. Her father carries a frameshift mutation, and her mother carries a splicing mutation. Conclusion The diagnosis of HFI caused by ALDOB mutation can be confirmed by high-throughput sequencing technology.

Next generation sequencing to promote the diagnosis and treatment of rare genetic diseases / 中华检验医学杂志

Next generation sequencing (NGS) based test provided us an unprecedented power for the molecular diagnosis of rare diseases with genetic etiology, thus enabling the practice of precision medicine.In order to maximize the clinical utilities of NGS-based test, attention should be paid to the improvement of the sequencing technology, data quality and the accuracy of data interpretation, as well as the clinical correlations and pre-and post-test genetic counseling services.In doing so, it is believed practice of NGS-based test can bring expected benefit to many patients and families.

Clinical-grade gene curation strategy in the development of short stature related gene panel by next generation sequencing / 中华检验医学杂志

Objective Design short stature panel with gene curration strategy.Methods The gene curation process was introduced in detail.The strength of a gene-disease relationship was evaluated based on publicly available genetic and experimental evidence.This process in short stature panel design and its effect on gene selection was further demonstrated.Results After gene curation, the number of gene in list was effectively decreased from 1 276 to 705.The panel sequencing reached a diagnosis rate of 19.7% among a cohort of 371 nation-wide ascertained short stature patients.The gene curation process reduced the risk of false positive findings and decreased diagnostic cost and working hours without affecting the diagnosis rate.Conclusion Gene curation is an important step for NGS-based test and should be widely exercised.

The Treatment Experience of Elderly AML Patients after Chemotherapy with TCM by SHEN Yiping / 浙江中医药大学学报

[Purpose] To summarize SHEN Yiping's clinical experience and academic views about treatment of elderly acute myeloid leukemia(AML) patients with traditional Chinese medicine(TCM).[Method] By means of learning form Professor SHEN in the clinic,collect cases and analyze them,and then conclude his clinical thought and dialectical methods,further summarize his clinical experience and academic views.[Result] Professor SHEN Yiping believes that these patients have deficiency of the lung,spleen and kidney,easily form the unhealthy environmental influences with shapes such as phlegm,damoeness,blood stasis,meeting with invaded by the invasion,causing the results of the happening of the disease.The functions of Zang-fu are damaged after chemotherapy,with the presentation of deficiency of qi and yin.Professor SHEN thinks that the treatment should be tonifying lung,spleen and kidney,dispelling the pathological products such as phlegm,dampness,blood stasis,eliminating the invasion at the same time.For those patients who are in remission,we should use the therapy of purging fire and maintaining yin,in order to remove leukemia residual of lesions thoroughly.Professor SHEN uses the anticancer drugs which could clear away heat and toxic frequently in order to depress the proliferation of the leukemia cells.[Conclusion]Professor SHEN is well-versed in the learning of both TCM and modern medicine,abundant clinical experience and rigorous dialectical methods,skilled in using TCM to treat elderly AML patients.He also has peculiar methods for the treatment of patients with recurrence of leukemia.His clinical experience and academic thoughts are worth learning and communication for us.

Genome-wide copy number variations analysis in 64 patients with unexplained intellectual disability / 中华实用儿科临床杂志

Objective To investigate the genetic basis of patients with intellectual disability,and to assess the application of single nucleotide polymorphisms (SNP)-array in the molecular diagnosis of intellectual disability.Methods Sixty-four patients with intellectual disability who were identified in Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region from January 2013 to June of 2015 were enrolled.Genomic DNA was extracted from peripheral blood and was analyzed with Illumina Humancyto SNP-12 300K gene array chip.All identified copy number variants (CNVs) were analyzed with references from databases such as ClinVar,DECIPHER,OMIM and DGV(Database of Genomic Variants),as well as comprehensive literature review from PubMed database to determine the pathogenicity of CNVs.Results Sixteen cases of the above 64 patients were found to have CNVs with genomic alterations,including 6 cases microdeletions/microduplications associated with known syndromes,3 cases microdeletions and microduplications with clear clinical relevance (non-syndrome),1 case numerical chromosome aberration,1 case unbalanced translocation and 5 cases CNVs of unknown clinical significance.The detection rate was 25% (16/64 cases).Among these 16 abnormalities,6 cases of them could not be detected by using karyotyping analysis because their sizes were less than 5 Mb,and the smallest detected missing fragment was 0.53 Mb.Conclusion SNP-array gene chip technique with the advantages of higher efficiency,high-resolution and good accuracy,which can be applied to the genetic diagnosis of intellectual disability.

The clinical manifestation and gene mutation of primary renal glucosuria in a child / 临床儿科杂志

Objective To explore the clinical manifestation and gene mutation of primary renal glucosuria (PRG). Methods The clinical data and gene detection results of a child with PRG were analyzed. Results A girl aged 2 years and 10 mouths had glucose ++++ by urine dipstick analysis and 22.4 g of the 24 h urine glucose. Her father was urine glucose positive. Genome DNA was extracted from peripheral blood of the girl and her parents, SLC5A2 gene were amplified by PCR for sequencing, including exons and splicing areas. The results showed a homozygous point mutation (c.127-16C>A) in girl, and both of her patents had the same heterozygous mutation. This mutation had been classified to pathogenic mutations by ClinVar data base. Conclusions The diagnosis of PRG is confirmed in this child and SLC5A2 gene mutation is the cause.

Alstrom syndrome in children:a case report and literature review / 临床儿科杂志

Objective To analyze the clinical feature, diagnosis and treatment of Alstrom syndrome. Method The clinical data of a case of Alstrom syndrome and the result of her ALMS1 sequencing by the two generation sequencing were retrospectively reviewed. Results The 12 year and 10 month old female suffered from dilated cardiomyopathy, obesity, optic nerve diseases, sensorineural hearing loss, high blood glucose and irregular menstruation since one month of birth. Laboratory examination showed she had high testosterone level, hyperglycemia, hyperlipidemia and fatty liver. High-throughput sequencing confirmed there was ALMS1 gene mutation which includes hybrid frameshift mutations of c.5418delC and p.Y1807Tfs*23, and heterozygous nonsense mutation of c.10549C>T and p.Q3517*, and c.5418delC was a new variation reported for the first time. Conclusion Alstrom syndrome is an autosomal recessive genetic disease, which is characterized by multiple organ dysfunction and metabolic syndrome, and can be diagnosed by gene detection.

Novel compound heterozygous mutations of the PCNT gene in one Chinese boy with microcephalic osteodysplastic primordial dwarfism typeⅡ:case report and literature review / 中华内分泌代谢杂志

[Summary] Microcephalic or Majewski's osteodysplastic primordial dwarfism type Ⅱ ( MOPD Ⅱ) is an extremely rare genetic disease mainly caused by pericentrin ( PCNT) gene mutations. This paper reported one 13-year-old boy, who was admitted because of the slow growth for more than 13 years and deepened skin color over six months. He was diagnosed as MOPD Ⅱ associated with a combination of growth hormone deficiency, type 2 diabetes, hypertension, acanthosis nigricans, multiple café-au-lait spots. On magnetic resonance imaging of brain, no vascular malformations such as aneurysms were shown. There were novel compound heterozygous mutations of PCNT gene in the patient, with the nonsense mutations of c. 502C > T ( p. Gln168 * heterozygous variation) and c. 3103C > T (p. Arg1035* heterozygous variation). His father carried a nonsense mutation c. 3103C > T ( p. Arg1035 *heterozygous variation ) and his mother had a nonsense mutation c. 502C > T ( p. Gln168 * heterozygous variation). After treatment with metformin for three months, his blood glucose returned to normal, and acanthosis nigricans was improved. It seems critical to evaluate the abnormal condition of blood vessels regularly for MOPD Ⅱpatients with PCNT gene mutations.

A boy with Meier-Gorlin syndrome carrying a novel ORC6 mutation and uniparental disomy of chromosome 16 / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To identify the genetic cause for a 11-year-old Chinese boy with Meier-Gorlin syndrome (MGS).</p><p><b>METHODS</b>Chromosomal microarray analysis (CMA) was used to detect potential variations, while whole exome sequencing (WES) was used to identify sequence variants. Sanger sequencing was used to confirm the suspected variants.</p><p><b>RESULTS</b>The boy has featured short stature, microtia, small patella, slender body build, craniofacial anomalies, and small testes with normal gonadotropin. A complete uniparental disomy of chromosome 16 was revealed by CMA. WES has identified a novel homozygous mutation c.67A>G (p.Lys23Glu) in ORC6 gene mapped to chromosome 16. As predicted by Alamut functional software, the mutation may affect the function of structural domain of the ORC6 protein.</p><p><b>CONCLUSION</b>The patient is probably the first diagnosed MGS case in China, who carried a novel homozygous mutation of the ORC6 gene and uniparental disomy of chromosome 16. The effect of this novel mutation on the growth and development needs to be further investigated.</p>

The correlation between phenotype and genotype of 5α-reductase 2 deficiency in 5 children / 临床儿科杂志

Objective To explore the correlation between phenotype and genotype of 5α-reductase 2 deficiency. Methods The clinical data of five children with 5α-reductase 2 deficiency were retrospectively analyzed and the relation between their clinical phenotype and genotype were analyzed. Results All of these five children presented small penis and testicular hypoplasia, three of whom had ones similar to the clitoris appearance. The testosterone/dihydrotestosterone (T/DHT) ratio was 10.26-64.99 after human chorionic gonadotropin (hCG) stimulation. Gene detection showed one case had c.680G>A homozygous mutation and the others were compound heterozygous mutations. The mutations were mainly missense mutations, followed by deletion, duplication and nonsense mutations. Conclusion The 5α-reductase 2 deficiency has different degrees of abnormal genital development. Genetic testing contributed to the diagnosis of this disease.