Heterozygous Deletion Of Exon Research Articles

Generation and characterization of induced pluripotent stem cell (iPSC) lines of two asymptomatic individuals carrying a heterozygous exon 7 deletion in Parkin (PRKN) and two non-carriers from the same family

Mutations in the Parkin (PRKN) gene are the most frequent known cause of autosomal recessive early-onset Parkinson’s disease (PD). Heterozygous mutations might predispose to disease with a highly reduced penetrance. We generated iPSC lines from two individuals carrying a heterozygous deletion of exon 7 in the PRKN gene and two controls from the same family. PBMCs were reprogrammed using non-integrating episomal plasmids. The iPSC lines exhibit expression of pluripotency markers, the potential to differentiate into the three germ layers, and a stable karyotype. These lines will serve to study mechanisms of reduced penetrance in heterozygous PRKN mutation carriers.

A novel synonymous ABCA3 variant identified in a Chinese family with lethal neonatal respiratory failure

BackgroundLethal respiratory failure is primarily caused by a deficiency of pulmonary surfactant, and is the main cause of neonatal death among preterm infants. Pulmonary surfactant metabolism dysfunction caused by variants in the ABCA3 gene is a rare disease with very poor prognosis. Currently, the mechanisms associated with some ABCA3 variants have been determined, including protein mistrafficking and impaired phospholipid transport. However, some novel variants and their underlying pathogenesis has not been fully elucidated yet. In this study we aimed to identify the genetic features in a family with lethal respiratory failure.MethodsWe studied members of two generations of a Chinese family, including a female proband, her parents, her monozygotic twin sister, and her older sister. Trio whole exome sequencing (WES) were used on the proband and her parents to identify the ABCA3 variants. Sanger sequencing and real-time quantitative polymerase chain reaction (PCR) were used on the monozygotic twin sister of proband to validate the ABCA3 synonymous variant and exon deletion, respectively. The potential pathogenicity of the identified synonymous variant was predicted using the splice site algorithms dbscSNV11_AdaBoost, dbscSNV11_RandomForest, and Human Splicing Finder (HSF).ResultsAll patients showed severe respiratory distress, which could not be relieved by mechanical ventilation, supplementation of surfactant, or steroid therapy, and died at an early age. WES analysis revealed that the proband had compound heterozygous ABCA3 variants, including a novel synonymous variant c.G873A (p.Lys291Lys) in exon 8 inherited from the mother, and a heterozygous deletion of exons 4–7 inherited from the father. The synonymous variant was consistently predicted to be a cryptic splice donor site that may lead to aberrant splicing of the pre-mRNA by three different splice site algorithms. The deletion of exons 4–7 of the ABCA3 gene was determined to be a likely pathogenic variant. The variants were confirmed in the monozygotic twin sister of proband by Sanger sequencing and qPCR respectively. The older sister of proband was not available to determine if she also carried both ABCA3 variants, but it is highly likely based on her clinical course.ConclusionsWe identified a novel synonymous variant and a deletion in the ABCA3 gene that may be responsible for the pathogenesis in patients in this family. These results add to the known mutational spectrum of the ABCA3 gene. The study of ABCA3 variants may be helpful for the implementation of patient-specific therapies.

Identification of multi-exon deletion in the COL7A1 gene underlying dystrophic epidermolysis bullosa by whole-exome sequencing

Dystrophic epidermolysis bullosa (DEB) is a rare form of genodermatosis characterized by skin blisters, milia, scarring over the entire body, and nail dystrophy. In this study, a pedigree with one affected member with skin blisters, and a clinical diagnosis of epidermolysis bullosa who was a result of a non-consanguineous marriage, was investigated by whole-exome sequencing (WES). This survey revealed that the proband is a compound heterozygote for a previously reported heterozygous missense variant (c.6205C>T) and a heterozygous deletion of exons 13–24 in the COL7A1 gene. This study indicates that the use of WES along with copy number variation (CNV) analysis gives a higher diagnostic yield for such patients. Moreover, considering the autosomal recessive and dominant forms of the disease, both caused by variants in one gene, proper interpretation and classification of novel variants in heterozygous as well as homozygous states is always a major challenge.

Maturity Onset Diabetes of the Young Masquerading as New Onset Diabetes Mellitus Type 1

Introduction:/background: Maturity-onset diabetes of the young (MODY) is a heterogeneous group of monogenic disorders with autosomal dominant mode of inheritance. Mutation in hepatocyte nuclear factor-1β (HNF-1β) gene results in an error of embryonic development of pancreas and nephron, leading to MODY type 5. MODY 5 accounts for 1% of maturity-onset diabetes of the young. It has peak incidence in adolescence/early adulthood, and is associated with renal pathology. Clinical Case: A 15-year boy with history of hypertension and Hashimoto thyroiditis with normal thyroid function was referred for Hb A1C of 6.7% (< 6.4%). Physical exam was remarkable for normal weight at 64%, normal BMI at 83%, absence of thyromegaly or acanthosis nigricans. Diabetes was confirmed by 2 hour Oral Glucose Tolerance Test study (baseline glucose 154 mg/dL (<126 mg/dL), 2 hour glucose 384 mg/dL (<140 mg/dL)). Small doses of insulin (total daily dose 0.1 units/kg/day) resulted in good glucose control. Further labs were significant for weakly positive TTG and GAD antibodies (tTG Ab IgA 55.5 U/mL (<4.0 U/mL), GAD-65 Ab 0.05 nmol/L (< 0.02 nmol/L)), positive TPO (0.0 - 34.9 IU/mL) and detectable ATA antibodies 45.8 IU/mL (0.0 - 40.0 IU/mL), C-peptide 2.9 ng/mL (0.9–7.1 ng/mL). Islet cell, Insulin and Zinc transporter 8 antibodies were negative. Over the next few months he was weaned off insulin and subsequently he had a high insulin of 29.43 uU/mL (3.0 - 17.0 uU/mL) with glucose level of 169 mg/dL. Renal US was performed as part of the work up for hypertension and revealed a small right calculus with no hydronephrosis and a small 8-mm cortical cyst in the right kidney. Urinalysis showed microalbuminuria. Upper GI endoscopy and colonoscopy with biopsy ruled out celiac disease. Presumptive diagnosis of MODY was entertained despite positive TPO, ATA, TTG and GAD antibodies suggesting autoimmune endocrinopathies. His Hb A1C levels were in the range of 5.7 to 6 % during the 15 months of follow up. Genetic testing for MODY resulted in heterozygous deletion of exons 1–9 of the HNF1B gene consistent with MODY5. Conclusion: This is a case of MODY 5 with weakly positive GAD 65 antibodies that was initially misdiagnosed as type 1 diabetes. The presence of weakly positive antibodies should not preclude a work up for MODY in a patient who does not have the clinical features of classic type 1 DM.

Pathologically and Genetically Diagnosed Subclinical Symptomatic Duchenne Muscular Dystrophy Carrier: Broadened Spectrum of Clinical Phenotype

A 29-year-old female presented with an elevated level of serum creatine kinase without subjective weakness. Neurologic examination showed the subtle motor weakness of the right arm. Muscle biopsy showed dystrophic changes and a mosaic pattern of dystrophin expression. The diagnosis was confirmed by multiplex ligation-dependent probe amplification and whole-exome sequencing, revealing heterozygous deletion of exon 44 in the DMD gene. Here, we introduce a subclinical symptomatic Duchenne muscular dystrophy carrier, which broadens the clinical spectrum of phenotype.

A Case Report on Congenital Hyperinsulinism

Introduction: Congenital hyperinsulinism (CH) is the most common reason for persistent hypoglycemia in neonates. Insulin levels increased inappropriately in the presence of hypoglycemia. Initial management is nonsurgical, but if it fails then partial pancreatectomy is done, which is a surgical procedure. Objective: To report newborn with CH and update medical and/or surgical treatment. Case report: It is reporting of a term newborn with severe symptomatic hypoglycemia not responding to medical treatment. Gene study was done—ABCC8 gene has been identified as homozygous deletion of exon 13 and parents ger08Y—showing heterozygous deletion of exon 13. Genetic study was consistent with focal CH. Discussion: This report presents diagnosis and clinical features of CH.

Clinical and Molecular Analysis of Four Patients With 11β-Hydroxylase Deficiency.

Objective: 11β-hydroxylase deficiency (11βOHD) is a rare autosomal recessive disorder caused by mutations in the CYP11B1 gene. It is characterized by virilization, hypertension, and significant final height impairment. In this study, we aim to investigate the clinical and molecular characteristics of four unrelated Chinese patients with 11βOHD disorder.Methods: The clinical information of four 11βOHD patients were carefully reviewed. Genetic analysis was performed using next-generation sequencing (NGS) based panel analysis. NGS coverage depth was analyzed to detect exonic copy-number variants (CNVs) on patient 1. Quantitative PCR (qPCR) was subsequently performed to confirm the CNVs detected from the NGS coverage depth analysis.Results: The mean age of the patients at diagnosis was 4.7 years (range, 2.0–9.3 years). Two genetically female patients (patients 1 and 2) with 11βOHD presented severe virilization of external genitalia and were raised as males. Two genetically male patients (patients 3 and 4) presented precocious puberty. Additionally, patients 1, 3, and 4 presented with hypertension. In patient 4, unilateral adrenal mass was detected and removed at the age of 9 years. Interestingly, the height of patient 4 (174.4 cm, +6.7 SD) wasn't impaired and reached his mid-parental height (173 cm). Three novel variants in the CYP11B1 gene (c.1150_1153del, c.217C>T, and c.400G>C) were identified by NGS. Various bioinformatics tools revealed potential pathogenic effects for the novel variants, and evolutionary-conservation revealed that the novel missense variant affected an amino acid that is highly conserved among species. Furthermore, NGS coverage depth analysis and qPCR identified a novel heterozygous deletion of exons 1–6 in patient 1.Conclusion: Our study expands the spectrum of mutations of the CYP11B1 gene in Chinese population. In addition, We reported the first case of a patient with classical 11βOHD disorder, whose final height wasn't compromised.

Differential diagnosis of vacuolar myopathies in the NGS era.

Altered autophagy accompanied by abnormal autophagic (rimmed) vacuoles detectable by light and electron microscopy is a common denominator of many familial and sporadic non‐inflammatory muscle diseases. Even in the era of next generation sequencing (NGS), late‐onset vacuolar myopathies remain a diagnostic challenge. We identified 32 adult vacuolar myopathy patients from 30 unrelated families, studied their clinical, histopathological and ultrastructural characteristics and performed genetic testing in index patients and relatives using Sanger sequencing and NGS including whole exome sequencing (WES). We established a molecular genetic diagnosis in 17 patients. Pathogenic mutations were found in genes typically linked to vacuolar myopathy (GNE, LDB3/ZASP, MYOT, DES and GAA), but also in genes not regularly associated with severely altered autophagy (FKRP, DYSF, CAV3, COL6A2, GYG1 and TRIM32) and in the digenic facioscapulohumeral muscular dystrophy 2. Characteristic histopathological features including distinct patterns of myofibrillar disarray and evidence of exocytosis proved to be helpful to distinguish causes of vacuolar myopathies. Biopsy validated the pathogenicity of the novel mutations p.(Phe55*) and p.(Arg216*) in GYG1 and of the p.(Leu156Pro) TRIM32 mutation combined with compound heterozygous deletion of exon 2 of TRIM32 and expanded the phenotype of Ala93Thr‐caveolinopathy and of limb‐girdle muscular dystrophy 2i caused by FKRP mutation. In 15 patients no causal variants were detected by Sanger sequencing and NGS panel analysis. In 12 of these cases, WES was performed, but did not yield any definite mutation or likely candidate gene. In one of these patients with a family history of muscle weakness, the vacuolar myopathy was eventually linked to chloroquine therapy. Our study illustrates the wide phenotypic and genotypic heterogeneity of vacuolar myopathies and validates the role of histopathology in assessing the pathogenicity of novel mutations detected by NGS. In a sizable portion of vacuolar myopathy cases, it remains to be shown whether the cause is hereditary or degenerative.

1748-P: One Novel 7.2kb Deletion in Exon 8 of INSR Gene in Diabetic Qatari Female with Type A Insulin Resistance Syndrome: The 1000 Qatar-Omics Study Cohort

Background: A 46-year-old Qatari female with a BMI of 25kg/m2 presented with hyperglycemia (blood glucose 13.5 mmol/l), hyperinsulinemia (21µU/mL) with elevated levels of HbA1c (10.3mmol/l). Biochemical investigations showed raised serum C-peptide (2.02ng/ml) and triglycerides (2.07mmol/L) and uric acid (104mg/dL), with normal BP. The objective of this case study is to validate this variant found through WGS in insulin receptor (INSR) gene that play a major cause of insulin resistant syndrome with different spectrums. Methods: Structural Variants discovered using custom multi-algorithm pipeline developed and optimized to run on HPC for short-read WGS data. In brief, 10 software packages applied (Breakdancer, Breakseq2, CNVnator, Delly, ERDS, Genomestrip, Manta, Speedseq, Svaba, WHAM), to existing short-read data. SVs annotated using AnnotSV and provides us functionally, regulatory and clinically relevant information. SVs analyzed based on their properties like pli-score, overlaps with known databases and OMIM annotations. This deletion was validated by ddPCR and the molecular docking performed by the autodock suit in order to understand the effect of deletion in the interaction between this receptor and insulin. Results: The patient was identified with 7.2k heterozygous deletion in exon 8 of INSR gene which play an essential role in the formation of extracellular alpha subunits in insulin receptor. molecular docking proved the decrease of catalytic activity of INSR and, hence signaling. Considering this and the phenotypic data from Qatar biobank, the patient developed features of type A insulin resistant syndrome as consequence of persistence hyperinsulinemia. The patient also exhibits severe Deterioration of glucose tolerant even with medication and unfortunately developed nephropathy. Conclusion: We highlighted the power of NGS in precise diagnosis and developing a potential and promising targeted therapeutics. Disclosure A.S. Akil: None. E.A.M. Yassin: None. S. Subash Padmajeya: None. L.A. Jerman: None. A. Fadda: None. W.H.O. Aamer: None. E.E. Aliyev: None. K. Fakhro: None.

Chinese patient with neurofibromatosis-Noonan syndrome caused by novel heterozygous NF1 exons 1\u201358 deletion: a case report

BackgroundNeurofibromatosis-Noonan syndrome (NFNS) is a rare autosomal dominant hereditary disease. We present a case of NFNS due to the heterozygous deletion of exons 1–58 of the NF1 gene on chromosome 17 in a 15-month-old boy.Case presentationA 15-month-old boy was admitted for motor and language developmental delay, numerous café-au-lait spots, hypertelorism, left blepharoptosis, pectus excavatum, cryptorchidism, secondary atrial septal defect, and UBOs (undefined bright objects) revealed by cranial MRI T2FLAIR in basal ganglia and cerebellum. Using whole exome sequencing, we identified a de novo heterozygous deletion including exons 1–58 of the NF1 gene.ConclusionAlthough genetic tests are useful tools for diagnosis of NFNS, NF1, or NS, comprehensive analysis of genetic factors and phenotypes is indispensable in the clinical practice. To the best of our knowledge, this case presents the first Chinese NFNS case due to NF1 defects, and the NF1 exons 1–58 deletion-related phenotype is unlike any other reported case.

CPEB1 deletion is not a common explanation for premature ovarian insufficiency in a Chinese cohort

PurposePremature ovarian insufficiency (POI), which is characterized by early menopause before the age of 40 years, affects approximately 1–5% of women. Cytoplasmic polyadenylation element binding protein 1 (CPEB1) is a post-transcriptional regulatory protein that is highly expressed in germ cells and promotes oocytes maturation, and several studies have found microdeletions of chromosome 15q25.2, which contains the CPEB1 gene, in POI patients. However, the deleted region also includes other plausible genes, and thus the contribution of CPEB1 to POI is uncertain. The present study aimed to determine the relationship between CPEB1 deletion and POI in a Chinese cohort.Material and methodsQuantitative real-time polymerase chain reaction (qPCR) with primers for exon 4 and exon 11 of CPEB1 was performed to detect the CPEB1 deletion in 323 patients with POI and in 300 healthy controls. Subsequent qPCR with primers for each exon of CPEB1 was performed to precisely localize the deletion locus.ResultsOne patient with primary amenorrhea was found to carry a heterozygous deletion of exons 8–12 of the CPEB1 gene.ConclusionOur study is the first to search for CPEB1 deletions in POI patients using a simple qPCR method, and we show that CPEB1 deletion is not a common cause for POI in a Chinese cohort.

Novel HADHB mutations in a patient with mitochondrial trifunctional protein deficiency

We encountered a patient with mitochondrial trifunctional protein deficiency in whom the corresponding mutations were not identified by a DNA panel for newborn screening for targeted diseases. After diagnosis confirmation by an enzyme assay and immunoblotting using the autopsied liver, the re-evaluation of the panel data indicated a heterozygous deletion of exons 6–9 that was later confirmed at the genomic level. cDNA analysis also identified exonization of the 5′ region of intron 9 caused by a deep intronic mutation, c.811 + 82A>G.

Genetic analysis of 90 families affected with spinal muscular atrophy

To carry out genetic testing and prenatal diagnosis for 90 families affected with spinal muscular atrophy (SMA), and discuss the necessity for carrier screening. All families were subjected to multiplex ligation-dependent probe amplification (MLPA) analysis. Combined MLPA and allele-specific PCR (AS-PCR) was used for prenatal diagnosis of the pregnant women. Among the 90 couples, 84 (93%) had a negative family history, 85 (94%) had given birth to an affected child before. Eighty-five husbands and 88 wives carried heterozygous deletion of exon 7 of the SMN1 gene. Two wives had homozygous deletion of exon 7 of the SMN1 gene and were affected. Prenatal diagnosis showed that 19 fetuses were SMA patients, 48 fetuses were carriers, and 23 fetuses were normal. Of note, eighteen affected fetuses were conceived by couples without a family history, which accounted for 20% of all pregnancies and 95% of all affected fetuses. To screen SMA carriers using MLPA and carry out prenatal diagnosis using combined MLPA and AS-PCR can ensure accurate diagnosis, which has a significant value for the prevention of SMA affected births.

Haploinsufficiency of A20 with a novel mutation of deletion of exons 2–3 of TNFAIP3

Objectives Haploinsufficiency of A20 (HA20) due to loss-of-function mutations of TNFAIP3 leads to an autoinflammatory disease. These mutations produce a premature termination codon in most cases of HA20. However, exon deletion has not been reported. Methods Genomic DNA was extracted from the peripheral blood of the patient clinically suspected of HA20. We examined autoinflammatory disease-causing genes and performed a multiplex ligation-dependent probe amplification (MLPA) assay for copy number analysis. Next, to determine the disconnection point, genomic DNA was amplified with long-range PCR and sequenced. Finally, western blotting was carried out to measure A20 protein expression in mitogen phytohaemagglutinin (PHA)-induced T-cell blasts from the patient and a healthy volunteer. Results Targeted next-generation sequencing found no pathogenic mutation, but copy number variation (CNV) analysis suggested a heterozygous deletion of exons 2–3. The MLPA assay and long-range PCR confirmed the mutation. Western blotting analysis indicated a marked decrease in expression of A20 protein from the patient compared to a normal control. The results showed that this deletion was a pathogenic mutation. Conclusion This study demonstrates a novel mutation resulting in a deletion of exons 2–3 of TNFAIP3. MLPA analysis is a useful initial screening method for HA20 patients.

Supplementary value of denaturing high performance liquid chromatography for routine prenatal diagnosis of spinal muscular atrophy by multiple ligation-dependent probe amplification

To explore the feasibility of high performance liquid chromatography (DHPLC) combined with multiple ligation-dependent probe amplification (MLPA) for the prenatal diagnosis of spinal muscular atrophy (SMA). Three families who had given birth to children with SMA type I were subjected to prenatal diagnosis. Peripheral blood samples were collected from the three couples, and 10 mL amniotic fluid was taken for each fetus through amniocentesis at 16-24 gestational week. Following DNA extraction, maternal contamination was excluded by STR analysis. Copy numbers of the SMN genes were detected by denaturing high performance liquid chromatography (DHPLC). Relative copy number of SMN1, SMN2 and reference genes was detected with a MLPA P021 assay kit. The three couples were all found to harbor heterozygous deletion of exon 7 of the SMN1 gene by DHPLC. MLPA analysis also suggested that the three couples were all carriers of SMA mutations. The fetus of family 1 harbored homozygous deletion of exons 7 and 8 of the SMN1 gene, in addition with heterozygous deletion of exons 7 and 8 of the SMN2 gene, suggesting that the fetus had SMA. The fetus of family 2 also harbored homozygous deletion of exons 7 and 8 of the SMN1 gene, while the copy number of SMN2 gene was normal, suggesting that the fetus was a SMA patient too. The fetus of family 3 harbored heterozygous deletion of exons 7 and 8 of the SMN1 gene, in addition with heterozygous deletion of exons 7 and 8 of the SMN2 gene, suggesting that the fetus was a carrier. DHPLC can effectively screen carriers of SMA mutations. Combined DHPLC and MLPA can provide accurate diagnosis for fetuses with a high risk for SMA.

Paroxysmal tonic upgaze: A heterogeneous clinical condition responsive to carbonic anhydrase inhibition.

Paroxysmal tonic upgaze (PTU), defined as an involuntary upward movement of the eyes, has been considered as a benign phenomenon but may also be associated with ataxia and developmental delay. We report eight children with PTU; six of them also exhibiting symptoms of ataxia and/or developmental delay. Treatment with carbonic anhydrase inhibition was offered to children with persisting and/or severe forms. Whole-exome sequencing and genome-wide array analysis (n=7) did not reveal mutations in the three known genes associated with PTU (CACNA1A, GRID2, SEPSECS), whereas by MLPA a heterozygous deletion of exon 31 of the CACNA1A gene could be detected in one patient, her mother and two further family members. Further exome and array analysis showed no recurrent variants in potentially novel PTU-related genes in more than one patient. A de novo variant at a highly conserved position in the SIM1 gene was detected in one patient, for which a pathogenic effect could be speculated. Carbonic anhydrase inhibition was started in five children and proved at least partially effective in all of them. Irrespective of the clinical background and the molecular basic mechanism of PTU, therapeutic carbonic anhydrase inhibition was effective in all five children (acetazolamide, n=3; sultiame, n=2) who received this treatment.

Han Chinese family with early-onset Parkinson's disease carries novel compound heterozygous mutations in the PARK2 gene.

PurposeTo identify deletions, duplications, and point mutations in 55 previously reported genes associated with Parkinson's disease (PD) and certain genes associated with tremor, spinocerebellar ataxia, and dystonia in a Han Chinese pedigree with early‐onset Parkinson's disease (EOPD).Patients and MethodsClinical examinations and genomic analyses were performed on six subjects belonging to three generations of a Han Chinese family. Target region capture and high‐throughput sequencing were used to screen these genes associated with PD, tremor, spinocerebellar ataxia, and dystonia. The multiplex ligation‐dependent probe amplification (MLPA) method was applied to detect rearrangements in PARK2 exons. Direct Sanger sequencing of samples from all subjects further verified the detected abnormal PRKRA, SPTBN2, and ATXN2 gene fragments.ResultsTwo family members were diagnosed with PD based on the clinical manifestations, imaging analyses. PARK2 gene heterozygous deletion of exon 3 and heterozygous duplication of exon 6 were identified in them (II‐3 and 4). A single heterozygous deletion of exon 3 in PARK2 was detected in II‐5 and III‐10. A single duplication of exon 6 in PARK2 was detected in I1. Both the heterozygous mutation c.2834G>A (p. R945H) in exon 16 and the heterozygous mutation c.1924 C>T (p. R642W) in exon 14 of the SPTBN2 gene were identified in II‐3, II‐4, and III‐10. The heterozygous mutation c.2989 C>T (p. R997X) in exon 24 of the ATXN2 gene was detected in II‐4 and II‐5, and the heterozygous mutation c.170 C>A (p. S57Y) in exon 2 of the PRKRA gene was detected in II‐3, II‐4, and III‐10. Other mutations in some genes associated with PD, tremor, spinocerebellar ataxia, and dystonia were not detected.ConclusionsNovel compound heterozygous mutations were identified in a Han Chinese pedigree and might represent a cause of EOPD.

Mosaic mutation in the NEMO gene causes incontinentia pigmenti in a male patient

Objective To identify mutations in the NEMO gene in a family with incontinentia pigmenti. Methods Clinical data were collected from the proband, and peripheral blood samples were obtained from the proband, her parents and 200 healthy controls. Multiplex PCR was performed to detect heterozygous deletion of exons 4-10 of the NEMO gene in the blood samples of the proband and her parents. Then, PCR was performed to amplify exons 2, 3-10 of the NEMO gene in all the blood samples, and all exons in the gene coding region and their flanking sequences were subjected to DNA sequencing. DNA was extracted from paraffin-embedded lesional tissue of the proband′s father, and PCR was performed to amplify exon 10 of the NEMO gene and its flanking sequence followed by DNA sequencing. Results The deletion of exons 4-10 of the NEMO gene was undetected in the peripheral blood of the proband or her father. Sanger sequencing showed that there was a heterozygous mutation c.1236dupA in exon 10 of the NEMO gene in the peripheral blood of the proband, which led to a mutation in amino acid residues (p. H413fs*7) . The c.1236dupA mutation was not found in the peripheral blood of the proband′s parents, while a mosaic mutation c.1236dupA was detected in the DNA from lesional tissues of the proband′s father. Conclusion The mutation c.1236dupA in the NEMO gene may be the underlying cause of incontinentia pigmenti in the proband and her father. Key words: Incontinentia pigmenti; DNA mutational analysis; Mosaicism; Skin manifestations; NEMO gene

Genetic study of a Parkinson's disease pedigree caused by compound heterozygous mutations in PARK2 gene

To explore the genetic basis for a Chinese pedigree where three siblings were affected with Parkinson's disease. Multiple ligation-dependent probe amplification (MLPA) and next-generation sequencing (NGS) were employed to detect the causative mutation. Sanger sequencing of cDNA was also used for verify the effect of mutation on the transcription of RNA. Heterozygous deletion of exon 3 of the PARK2 gene was detected by MLPA, while a heterozygous splice site variant c.619-3G>C was detected by NGS. Both mutations were shown to result in aberrant transcripts of the PARK2 gene (loss of exons 3 and 6, respectively) by Sanger sequencing of cDNA. Both mutations have co-segregated with the disease in the pedigree. Compound heterozygous mutations of the PARK2 gene probably underlie the disease in this pedigree. Identification of the splice site variant c.619-3G>C has expanded the mutation spectrum of the PARK2 gene.

Large-scale deletions of the ABCA1 gene in patients with hypoalphalipoproteinemia

Copy-number variations (CNVs) have been studied in the context of familial hypercholesterolemia but have not yet been evaluated in patients with extreme levels of HDL cholesterol. We evaluated targeted, next-generation sequencing data from patients with very low levels of HDL cholesterol (i.e., hypoalphalipoproteinemia) with the VarSeq-CNV® caller algorithm to screen for CNVs that disrupted the ABCA1, LCAT, or APOA1 genes. In four individuals, we found three unique deletions in ABCA1: a heterozygous deletion of exon 4, a heterozygous deletion that spanned exons 8 to 31, and a heterozygous deletion of the entire ABCA1 gene. Breakpoints were identified with Sanger sequencing, and the full-gene deletion was confirmed by using exome sequencing and the Affymetrix CytoScan HD array. Previously, large-scale deletions in candidate HDL genes had not been associated with hypoalphalipoproteinemia; our findings indicate that CNVs in ABCA1 may be a previously unappreciated genetic determinant of low levels of HDL cholesterol. By coupling bioinformatic analyses with next-generation sequencing data, we can successfully assess the spectrum of genetic determinants of many dyslipidemias, including hypoalphalipoproteinemia.