Establishment of a non-integrated iPSC (SDQLCHi068-A) line derived from a patient with autosomal dominant immunodeficiency-14A carrying a heterozygous mutation (c.3061G>A) in PIK3CD gene.

Phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta (PIK3CD) gene (OMIM#602839) encodes the p110δ catalytic subunit, mainly expressed in immune cells, and is associated with autosomal dominant immunodeficiency-14A with lymphoproliferation (IMD14A, #615513). We generated a human iPS cell line from a 50-month-old boy with IMD14A carrying a heterozygous mutation (c.3061G>A, p.E1021K) in PIK3CD gene. This cell line retains the original mutation site and shows differentiation potential towards three germ layers in vitro, which can be used as a disease model for research.

Generation and characterization of an induced pluripotent stem cell (iPSC) line SDQLCHi063-A from peripheral blood mononuclear cells of a patient with Maturity-onset diabetes of the young type 2 carrying GCK exon 1 deletion.

Maturity-onset diabetes of the young type 2 (MODY2) is an autosomal dominant disorder caused by mutations in the GCK gene. It is characterized by a non-progressive slight increase in glycosylated hemoglobin (HbA1c), and mildly raised fasting glucose. Here, we generated an induced pluripotent stem cell line SDQLCHi063-A from a five-year-old boy with MODY2 carrying exon 1 deletion of the GCK gene (OMIM*138079). The iPSC line carries original gene mutation, expresses pluripotency markers, has normal karyotype and differentiated spontaneously in the three germ layers.

Human induced pluripotent stem cell line (SDQLCHi064-A) derived from a patient with Canavan disease carrying c.556_559dup GTTC and c.919delA mutations in the ASPA gene.

Canavan disease (CD, OMIM# 271900) is an autosomal recessive neurodegenerative disorder caused by homozygous or compound heterozygous mutations in ASPA gene, which result in catalytic deficiency of the aspartoacylase enzyme and the accumulation of N-acetylaspartic acid (NAA). Clinical presentation varies according to the age of disease onset. Here, we generated a human induced pluripotent stem cell line (hiPSCs) SDQLCHi064-A from a 5-month old boy with CD carrying two novel frame shift mutations c.556_559dupGTTC (p.L187Rfs*5) and c.919delA (p.S307Vfs*24) of the ASPA gene, in order for us to better understanding the disease.

Establishment of iPS cell line (SDQLCHi061-A) from a patient with carbamoylphosphate synthetase I deficiency due to CPS1 mutation.

The induced pluripotent stem cells (iPSCs) line was generated using peripheral blood mononuclear cells (PBMCs) from a patient with compound heterozygous mutation of c.2374A > G/p.M792V and c.3949C > T/p.R1317W in the CPS1 gene by non-integrating vectors. The expression of pluripotency markers, potential for in vitro trilineage differentiation and exhibiting normal karyotype were demonstrated in the SDQLCHi061-A cell line. This cell line could provide a useful CPS1D model in vitro for further study.

Establishment of a non-integrated iPSC line (SDQLCHi043-A) from a male infant with propionic acidemia carrying compound heterozygote mutations in PCCB gene.

In this study, peripheral blood mononuclear cells were contributed from a male infant with propionic acidemia (PA) verified by clinical and genetic diagnosis, who inherited compound heterozygous mutations in the propionyl-CoA carboxylase subunit beta (PCCB) gene. Here, this iPS was generated by non-integrated episomal vectors with SOX2, BCL-XL, OCT4, C-MYC and OCT4. Also, this iPSC line exhibited the morphology of pluripotent stem cells, upward mRNA and protein expression of pluripotency markers, conspicuous in vitro differentiation potency and regular karyotype, and carried PCCB gene mutations, which provided an excellent model for the research and drug screening of PA.

Generation of a human induced pluripotent stem cell line (SDQLCHi057-A) from an Isovaleric aciduria patient carrying novel compound heterozygous mutations in the IVD gene.

Isovaleric acidemia (IVA; OMIM ID#243500) is an inborn error of leucine metabolism caused by a deficiency of isovaleryl-CoA dehydrogenase (IVD). In this study, we generated a human induced pluripotent stem cell line (hiPSCs) SDQLCHi057-A from a 2-year-7-month old boy with IVA carrying two heterozygous missense mutations c.215A > G (p.N72S) and c.883A > G (p.M295V) of the IVD gene. Patient-specific hiPSCs provide a proper model for further understanding this rare disease.

DCX variants in two unrelated Chinese families with subcortical band heterotopia: Two case reports and review of literature.

Introduction: Subcortical band heterotopia (SBH) is a rare brain developmental malformation caused by deficient neuronal migration during embryogenesis. Published literature on pediatric SBH cases caused by DCX mutations is limited. Methods: The detailed clinical and genetic features of two pediatric SBH with DCX mutations were analyzed. The available literature on DCX mutations was reviewed. Results: Both patients were girls with varying degrees of developmental delay. Patient 1 was short in stature with peculiar facial features. Patient 2 had an early seizure onset and developed drug-resistant epilepsy. Whole-exome sequencing (WES) revealed two de novo heterozygous variants of DCX (NM_178153.3), including a novel missense variant of c.568A > G (p.K190E) in P1 and a reported nonsense variant of c.814C > T (p.R272*) in P2. We reviewed all the available literature regarding DCX mutations. A total of 153 different mutations have been reported, with the majority of 99 (64.7 %) being missense mutations. Conclusion: Our study expanded the mutational spectrum of DCX, which has important implications for the study of genotype-phenotype correlations. Furthermore, it provided insights to better understand SBH and genetic counseling.

An induced pluripotent stem cell line (SDQLCHi062-A) from a patient carrying a mutation in the PAX2 gene.

Focal segmental glomerulosclerosis 7 (FSGS7, # 616002) is a condition marked by significant proteinuria with or without features of nephrotic syndrome. Heterozygous mutations in the PAX2 gene on chromosome 10q24 can cause FSGS7. Here, we generated an induced pluripotent stem cell line SDQLCHi062-A from a thirteen -years-old boy with FSGS7 caused by heterozygous mutation (c.226 G>A, p.G76S) in the PAX2 gene (OMIM * 167409). The established iPSC line was validated by pluripotency markers expression, original gene mutation and demonstrated trilineage differentiation potential in vitro.

Generation of a transgene-free iPS cell line (SDQLCHi053-A) from a young girl carrying a heterozygous mutation (c.427C > T) in SYNGAP1 gene.

The pathogenic mutations of Synaptic Ras GTPase-activating protein 1 (SYNGAP1) gene (OMIM #603384) have been tightly associated with a neurodevelopmental disease, also called autosomal dominant mental retardation type 5 (MRD5, OMIM #612621). We generated a human iPS cell line from a 34-month-old young girl bearing a recurrent heterozygous mutation (c.427C > T) of SYNGAP1. This cell line has great performance in pluripotency and shows differentiation potential towards three germ layers in vitro.

Clinical and genetic features of luscan-lumish syndrome associated with a novel de novo variant of SETD2 gene: Case report and literature review.

Introduction: Luscan-Lumish syndrome (LLS) is currently recognized as a rarely-observed condition featured with overgrowth, macrocephaly, obesity, type I Chiari malformation, and linguistic retardation. So far, there have been only a few LLS cases registered worldwide, but with none of them reported from China. To acquire a deeper understanding on the clinical and genetic features of this disease, a Chinese boy with LLS caused by a heterozygous variant in SETD2 gene was investigated in the present study. Methods: The patient was clinically examined and the medical history of his family was collected. Genetic testing was performed to determine the genetic etiology. Results: The proband was a boy aged 5-year-7-month-old, who was referred to our hospital due to "being a slow learner in kindergarten". The child had a history of delayed motor and language development in comparison to his peers. After admission, physical examination revealed tall stature and macrocephaly as the major manifestation, in addition to a relatively lower rating in intelligence assessment as well as abnormal MRI images showing a slightly shorter corpus callosum accompanied by a mildly thinner corpus callosum body. Whole exome sequencing (WES) revealed a heterozygous c.2514_2516delTAG (p.Ser838del) variant in SETD2 gene, which was subsequently identified as a novel de novo variant. According to the standardized genetic variant classification published by the American College of Medical Genetics and Genomics (ACMG), the variant, with a pathogenicity analysis result indicating PS2 + PM2_Supporting + PM4, was determined to be likely pathogenic. Through literature review, the clinical phenotypes of the 15 LLS cases were summarized, including 8 cases of overgrowth (53%), 13 cases of macrocephaly (87%), 11 cases of developmental delay (73%), 8 cases of autism (53%), and 7 cases of special facial features (47%). Besides, abnormal craniocerebral MRI findings were noticed in 7 cases. Despite that the mutation sites of the 15 patients varied from case to case, they showed a uniformly distributed pattern throughout the whole SETD2 gene, including 5 missense mutations, 5 frameshift mutations and 5 non-sense mutations. Conclusion: LLS, not having been recognized till recent years, is identified as an autosomal dominant syndrome triggered by SETD2 gene mutation. As the first report of LLS in China, the case in our study was proved to be associated with a unique type of SETD2 gene mutation that has never been reported previously, which is believed to enrich the mutation spectrum of SETD2 gene and also, deepening the clinicians' understanding on the disease.

Establishment of an induced pluripotent stem cell (iPSC) line SDQLCHi045-A from peripheral blood mononuclear cells of a patient with Coffin-Siris syndrome 1 carrying a mutation in ARID1B gene.

Coffin-Siris syndrome 1 (CSS1) is a multiple malformation syndrome characterized by mental retardation associated with coarse facial features, hypertrichosis, sparse scalp hair, and hypoplastic or absent fifth fingernails or toenails. Mutations in the ARID1B gene are the most common cause of CSS1. Here, we generated an induced pluripotent stem cell line SDQLCHi045-A from a one-year-old girl with CSS1 caused by heterozygous mutation (c.1924C>T, p.Q642X) in the ARID1B gene (OMIM*135900). The established iPSC line was validated by pluripotency markers, original gene mutation and demonstrated trilineage differentiation potential in vitro.

Phenotype and genotype analyses of Chinese patients with autosomal dominant mental retardation type 5 caused by SYNGAP1 gene mutations.

Background: Autosomal dominant mental retardation type 5 (MRD5), a rare neurodevelopmental disorder (NDD) characterized by intellectual disability (ID), developmental delay (DD), and epilepsy predominantly, is caused by a heterozygous mutation in the SYNGAP1 gene. SYNGAP1 mutations have been rarely reported in the Chinese population. Here, we present an investigation of SYNGAP1 mutations in a clinical cohort with ID and DD in Shandong, a northern province in China, to further explore the genotype and phenotype correlations. Methods: A retrospective study was conducted on 10 children with SYNGAP1 mutations presenting ID, DD, and epilepsy who were diagnosed between January 2014 and May 2022. Clinical data and genetic tests were collected. Treatment and regular follow-ups were carried out to pay close attention to the prognosis of the patients. Results: We described 10 unrelated affected individuals with SYNGAP1 mutations, displaying ID, DD, epilepsy, or seizures. All mutations of SYNGAP1 in the 10 patients were de novo, except patient 3 whose father was unavailable, including five nonsense mutations, two frameshift mutations, two splicing mutations, and one codon deletion. Among these mutations, five were novel and the other five were previously reported. Significantly, all patients with epilepsy were sensitive to anti-seizure drugs, especially sodium valproate. Furthermore, rehabilitation training seemed to exert a more improved effect on motor development than language development for the patients. Conclusion The 10 patients carrying SYNGAP1 mutations were diagnosed as MRD5. Five novel genetic mutations were found, which expanded the mutational spectrum of the SYNGAP1 gene. The identification of these mutations in this study helps explore the relationship between genotypes and phenotypes and contributes to genetic counseling and therapeutic intervention for patients with MRD5.

A synonymous mutation in PI4KA impacts the transcription and translation process of gene expression.

Phosphatidylinositol-4-kinase alpha (PI4KIIIα), encoded by the PI4KA gene, can synthesize phosphatidylinositol-4-phosphate (PI-4-P), which serves as a specific membrane marker and is instrumental in signal transduction. PI4KA mutations can cause autosomal recessive diseases involving neurological, intestinal, and immunological conditions (OMIM:619621, 616531, 619708). We detected sepsis, severe diarrhea, and decreased immunoglobulin levels in one neonate. Two novel compound heterozygous mutations, c.5846T>C (p.Leu1949Pro) and c.3453C>T (p.Gly1151=), were identified in the neonate from the father and the mother, respectively. Sanger sequencing and reverse transcription polymerase chain reaction (RT-PCR) for peripheral blood and minigene splicing assays showed a deletion of five bases (GTGAG) with the c.3453C>T variant at the mRNA level, which could result in a truncated protein (p.Gly1151GlyfsTer17). The missense mutation c.5846T>C (p.Leu1949Pro) kinase activity was measured, and little or no catalytic activity was detected. According to the clinical characteristics and gene mutations with functional verification, our pediatricians diagnosed the child with a combined immunodeficiency and intestinal disorder close to gastrointestinal defects and immunodeficiency syndrome 2 (GIDID2; OMIM: 619708). Medicines such as immunomodulators are prescribed to balance immune dysregulation. This study is the first report of a synonymous mutation in the PI4KA gene that influences alternative splicing. Our findings expand the mutation spectrum leading to PI4KIIIa deficiency-related diseases and provide exact information for genetic counseling.

Generation of an induced pluripotent stem cell line (SDQLCHi044-A) from a patient with autosomal dominant mental retardation type 5 harboring heterozygous mutation in SYNGAP1 gene.

Autosomal dominant mental retardation type 5 (MRD5) is a rare neurodevelopmental disorder caused by mutations in the SYNGAP1 gene. Here, we established an induced pluripotent stem cell (iPSC) line from peripheral blood mononuclear cells (PBMCs) of a 30-month-old boy carrying a heterozygous mutation (c.2059C > T) in the SYNGAP1 gene. The iPSCs exhibited a normal karyotype, expressed pluripotency markers, and displayed differentiation potential in vitro.

Genotypic and phenotypic characteristics of 12 chinese children with glycogen storage diseases.

Background: Glycogen storage diseases (GSDs) are known as a group of disorders characterized by genetic errors leading to accumulation of glycogen in various tissues. Since different types of GSD can sometimes be clinically indistinguishable, next generation sequencing is becoming a powerful tool for clinical diagnosis. Methods: 12 patients with suspected GSDs and their parents were enrolled in this study. The clinical and laboratory data of the patients were reviewed. Causative gene variants were identified in the patients using whole exome sequencing (WES) and verified by Sanger sequencing. Results: Genetic testing and analysis showed that 7 patients were diagnosed with GSD II (Pompe disease), 2 patients with GSD III, 1 patient with GSD VI, and 2 patients with GSD IXα. A total number of 18 variants were identified in 12 patients including 11 variants in GAA gene, 3 variants in AGL gene, 2 variants in PYGL gene and 2 variants in PHKA2 gene, of which 9 variants were reported and 9 variants were novel. SIFT, Polyphen-2, Mutation Taster, and REVEL predicted the novel variants (except GAA c.1052_1075 + 47del) to be disease-causing. The 3D structures of wild/mutant type GAA protein were predicted indicating that variants p. Trp621Gly, p. Pro541Leu, p. Ser800Ile and p. Gly293Trp might affect the proteins function via destroying hydrogen bonds or conformational constraints. Neither liver size nor laboratory findings allow for a differentiation among GSD III, GSD VI and GSD IXα. Conclusion: Our study expanded the variation spectrum of genes associated with GSDs. WES, in combination with clinical, biochemical, and pathological hallmarks, could provide accurate results for diagnosing and sub-typing GSD and related diseases in clinical setting.

Chromosomal microarray analysis of 410 Han Chinese patients with autism spectrum disorder or unexplained intellectual disability and developmental delay.

Copy number variants (CNVs) are recognized as a crucial genetic cause of neurodevelopmental disorders (NDDs). Chromosomal microarray analysis (CMA), the first-tier diagnostic test for individuals with NDDs, has been utilized to detect CNVs in clinical practice, but most reports are still from populations of European ancestry. To contribute more worldwide clinical genomics data, we investigated the genetic etiology of 410 Han Chinese patients with NDDs (151 with autism and 259 with unexplained intellectual disability (ID) and developmental delay (DD)) using CMA (Affymetrix) after G-banding karyotyping. Among all the NDD patients, 109 (26.6%) carried clinically relevant CNVs or uniparental disomies (UPDs), and 8 (2.0%) had aneuploidies (6 with trisomy 21 syndrome, 1 with 47,XXY, 1 with 47,XYY). In total, we found 129 clinically relevant CNVs and UPDs, including 32 CNVs in 30 ASD patients, and 92 CNVs and 5 UPDs in 79 ID/DD cases. When excluding the eight patients with aneuploidies, the diagnostic yield of pathogenic and likely pathogenic CNVs and UPDs was 20.9% for all NDDs (84/402), 3.3% in ASD (5/151), and 31.5% in ID/DD (79/251). When aneuploidies were included, the diagnostic yield increased to 22.4% for all NDDs (92/410), and 33.6% for ID/DD (87/259). We identified a de novo CNV in 14.9% (60/402) of subjects with NDDs. Interestingly, a higher diagnostic yield was observed in females (31.3%, 40/128) compared to males (16.1%, 44/274) for all NDDs (P = 4.8 × 10-4), suggesting that a female protective mechanism exists for deleterious CNVs and UPDs.

Diagnostic application of exome sequencing in Chinese children with suspected inherited kidney diseases.

Background: Inherited kidney diseases (IKDs) are a group of kidney diseases characterized by abnormal kidney structure or function caused by genetic factors, but they are not easily diagnosed in childhood due to either nonspecific symptoms and signs or clinically silent symptoms in the early stages until the progressive stages, even end-stages. Early diagnosis of IKDs is very urgent for timely treatment and improving outcomes of patients. So far, the etiological diagnosis has been accelerated with the advance of clinical genetic technology, particularly the advent of next-generation sequencing (NGS) that is not only a powerful tool for prompt and accurate diagnosis of IKDs but also gives therapy guidance to decrease the risk of unnecessary and harmful interventions. Methods: The patients presenting with urinalysis abnormalities or structural abnormalities from 149 Chinese families were enrolled in this study. The clinical features of the patients were collected, and the potentially causative gene variants were detected using exome sequencing. The clinical diagnostic utility of the genetic testing was assessed after more detailed clinical data were analyzed. Result: In total, 55 patients identified having causative variants by exome sequencing were genetically diagnosed, encompassing 16 (29.1%) autosomal dominant IKDs, 16 (29.1%) autosomal recessive IKDs, and 23 (41.8%) X-linked IKDs, with 25 unreported and 45 reported variants. The diagnostic yield was 36.9%. The utility of the exome sequencing was accessed, 12 patients (21.8%) were confirmed to have suspected IKDs, 26 patients (47.3%) discerned the specific sub-types of clinical category, and 17 patients (30.9%) with unknown etiology or lack of typical manifestations were reclassified. Conclusion: Our study supported that genetic testing plays a crucial role in the early diagnosis for children with IKDs, which affected follow-up treatment and prognostic assessment in clinical practice. Moreover, the variant spectrum associated with IKDs was expanded.

Transmission of a Novel Imprinting Center Deletion Associated With Prader-Willi Syndrome Through Three Generations of a Chinese Family: Case Presentation, Differential Diagnosis, and a Lesson Worth Thinking About.

Prader-Willi syndrome (PWS) is a complex genetic syndrome caused by the loss of function of genes in 15q11-q13 that are subject to regulation by genomic imprinting and expressed from the paternal allele only. The main clinical features of PWS patients are hypotonia during the neonatal and infantile stages, accompanied by delayed neuropsychomotor development, hyperphagia, obesity, hypogonadism, short stature, small hands and feet, mental disabilities, and behavioral problems. However, PWS has a clinical overlap with other disorders, especially those with other gene variations or chromosomal imbalances but sharing part of the similar clinical manifestations with PWS, which are sometimes referred to as Prader-Willi syndrome-like (PWS-like) disorders. Furthermore, it is worth mentioning that significant obesity as a consequence of hyperphagia in PWS usually develops between the ages of 1 and 6 years, which makes early diagnosis difficult. Thus, PWS is often not clinically recognized in infants and, on the other hand, may be wrongly suspected in obese and intellectually disabled patients. Therefore, an accurate investigation is necessary to differentiate classical PWS from PWS-like phenotypes, which is imperative for further treatment. For PWS, it is usually sporadic, and very rare family history and affected siblings have been described. Here, we report the clinical and molecular findings in a three-generation family with a novel 550-kb microdeletion affecting the chromosome 15 imprinting center (IC). Overall, the present study finds that the symptoms of our patient are somewhat different from those of typical PWS cases diagnosed and given treatment in our hospital. The familial occurrence and clinical features were challenging to our diagnostic strategy. The microdeletion included a region within the complex small nuclear ribonucleoprotein polypeptide protein N (SNRPN) gene locus encompassing the PWS IC and was identified by using a variety of techniques. Haplotype studies suggest that the IC microdeletion was vertically transmitted from an unaffected paternal grandmother to an unaffected father and then caused PWS in two sibling grandchildren when the IC microdeletion was inherited paternally. Based on the results of our study, preimplantation genetic diagnosis (PGD) was applied successfully to exclude imprinting deficiency in preimplantation embryos before transfer into the mother's uterus. Our study may be especially instructive regarding accurate diagnosis, differential diagnosis, genetic counseling, and PGD for familial PWS patients.

Establishment of human induced pluripotent stem cell line (SDQLCHi040-A) from a patient with Infantile-onset inflammatory bowel disease carrying a homozygous mutation in IL10RA gene.

Infantile-onset inflammatory bowel diseases (IO-IBD) is a heterogeneous subgroup of IBD spectrum characterized by age of onset less than 2 years old. Mutations in interleukin-10 receptor A (IL10RA) is one of the major causes. Here, we generated a human induced pluripotent stem cell line SDQLCHi040-A from a 1-year-4-month-old girl with IO-IBD caused by homozygous mutation (c.301 C > T, p.R101W) in the IL10RA gene (OMIM*146933). The established iPSC line was validated by pluripotency markers, original gene mutation and demonstrated trilineage differentiation potential in vitro.

Mutational Characteristics of Causative Genes in Chinese Hereditary Spherocytosis Patients: a Report on Fourteen Cases and a Review of the Literature.

Background: Hereditary spherocytosis (HS), characterized by the presence of spherocytic red cells in peripheral blood, hemolysis, splenomegaly, jaundice, and gallstones, is a common form of inherited hemolytic anemia (HA). To date, five causative genes associated with HS have been identified, including ANK1, SPTB, SPTA1, SLC4A1, and EPB42. Methods: Clinically suspected patients with HS or undiagnosed HA from 14 Chinese families were enrolled in this study. We presented the patients' clinical features and identified the causative gene variants in these patients using whole exome sequencing (WES), with 10 novel and four reported mutations in the ANK1 and SPTB genes (seven mutations in ANK1 and seven in SPTB), individually. Then, we reviewed all available literature on Chinese HS patients from 2000 to 2020 in PubMed and Chinese Journals with genetic results and clinical information, to delineate gene mutation spectrum and potential correlation with phenotypes. Results: A total of 158 variants (including 144 in previous reports and 14 in this study) indicated that ANK1 (46%) and SPTB (42%) were the most frequently mutated genes in Chinese HS patients, followed by SLC4A1 (11%) and SPTA1 (1%), while no mutations in EPB42 was reported. Most of the mutations in ANK1 and SPTB were nonsense (26/73 in ANK1 and 32/66 in SPTB) and frameshift (20/73 in ANK1 and 15/66 in SPTB), while missense mutations (14/18) accounted for the majority in SLC4A1. The higher mutation frequency of ANK1 was found in its exon 8, 9, 26, and 28. The majority of mutations in SPTB were located in its exon 13, 15, and 18-30, whereas mutations in SLC4A1 were scattered throughout the entire region of the gene. Conclusion: Our study expanded the mutation spectrum of ANK1 and SPTB. Furthermore, we clarified the mutational characteristics of causative genes by reviewing all available literature on Chinese patients with HS.