Identification of rare genetic variants in patients with intellectual disability ( ID ) has been greatly accelerated by advances in next generation sequencing technologies. However, due to small numbers of patients, the complete phenotypic spectrum associated with pathogenic variants in single genes is still emerging. Among these genes is ZBTB18 ( ZNF238 ), which is deleted in patients with 1q43q44 microdeletions who typically present with ID , microcephaly, corpus callosum ( CC ) abnormalities, and seizures. Here we provide additional evidence for haploinsufficiency or dysfunction of the ZBTB18 gene as the cause of ID in five unrelated patients with variable syndromic features who underwent whole exome sequencing revealing separate de novo pathogenic or likely pathogenic variants in ZBTB18 (two missense alterations and three truncating alterations). The neuroimaging findings in our cohort ( CC hypoplasia seen in 4/4 of our patients who underwent MRI ) lend further support for ZBTB18 as a critical gene for CC abnormalities. A similar phenotype of microcephaly, CC agenesis, and cerebellar vermis hypoplasia has been reported in mice with central nervous system‐specific knockout of Zbtb18 . Our five patients, in addition to the previously described cases of de novo ZBTB18 variants, add to knowledge about the phenotypic spectrum associated with ZBTB18 haploinsufficiency/dysfunction.

Donor genotype for polymorphisms near IFNL3 influences hepatitis C virus (HCV) therapy responsiveness. This relationship has not been studied in a sample of HCV-infected living donor liver transplantation (LDLT) recipients in the United States (US). We investigated the association of donor and recipient genotypes near the IFNL3 gene at a large US liver transplant center. Recipient homozygosity for rs12979860 C was associated with increased sustained virologic response (SVR) in antiviral treatment-experienced patients pretransplant (P = 0.055). Consistently, donor homozygosity for rs12979860 C was also associated with increased SVR in patients who received post-transplant antiviral therapy (P = 0.048). Transplantation of an rs12979860 CC graft confers a favorable post-transplant antiviral response among HCV-positive recipients in an LDLT setting. Recipients with the favorable rs12979860 genotype receiving antiviral therapy before transplant are also more likely to achieve SVR. The effect of genotype status in the era of direct-acting antiviral agents will require future study.

Between 2001 and 2005, 6,166 females underwent cystic fibrosis (CF) carrier screening at our institution. Only 36% were Caucasian. We identified 143 carrier females and subsequently tested 85 of their partners. The observed carrier frequency was not significantly different than expected for any racial or ethnic group tested. We identified 6 positive couples (5 Caucasian, 1 Arab American) and 1 affected fetus. In just under 4 years, our institution spent approximately USD 334,000 on CF population screening. Comparing this to the lifetime medical cost for a CF patient, CF population-based carrier screening is cost effective at our institution, despite the high number of non-Caucasians being screened.

Background: Mutations in the E-cadherin (CDH1) gene are a well documented cause of hereditary diffuse gastric cancer (HDGC). Development of evidence based guidelines for CDH1 screening for HDGC have been complicated by its rarity, variable penetrance, and lack of founder mutations.Methods: Forty three new gastric cancer (GC) families were ascertained from multiple sources. In 42 of these families at least one gastric cancer was pathologically confirmed to be a diffuse gastric cancer (DGC); the other family had intestinal type gastric cancers. Screening of the entire coding region of the CDH1 gene and all intron/exon boundaries was performed by bi-directional sequencing.Results: Novel mutations were found in 13 of the 42 DGC families (31% overall). Twelve of these mutations occur among the 25 families with multiple cases of gastric cancer and with pathologic confirmation of diffuse gastric cancer phenotype in at least one individual under the age of 50 years. The mutations found include small insertions and deletions, splice site mutations, and three non-conservative amino acid substitutions (A298T, W409R, and R732Q). All three missense mutations conferred loss of E-cadherin function in in vitro assays. Multiple cases of breast cancers including pathologically confirmed lobular breast cancers were observed both in mutation positive and negative families.Conclusion: Germline truncating CDH1 mutations are found in 48% of families with multiple cases of gastric cancer and at least one documented case of DGC in an individual under 50 years of age. We recommend that these criteria be used for selecting families for CDH1 mutational analysis.

Purpose: We expect that the mutation panel currently recommended for preconception/prenatal CF carrier screening will be modified as new information is learned regarding the phenotype associated with specific mutations and allele frequencies in various populations. One such example is the I148T mutation, originally described as a severe CF mutation. After implementation of CF population-based carrier screening, we learned that I148T exists as a complex allele with 3199del6 in patients with clinical CF, whereas asymptomatic compound heterozygotes for I148T and a second severe CF mutation were negative for 3199del6.Methods: We performed reflex testing for 3199del6 on 663 unrelated specimens, including I148T heterozygotes, compound heterozygotes, and a homozygous individual.Results: Less than 1% of I148T carriers were also positive for 3199del6. Excluding subjects tested because of a suspected or known CF diagnosis or positive family history, 0.6% of I148T-positive individuals were also positive for 3199del6. We identified 1 I148T homozygote and 6 unrelated compound heterozygous individuals with I148T and a second CF variant (2 of whom also carried 3199del6). In addition, one fetus with echogenic bowel and one infertile male were heterozygous for I148T (3199del6 negative).Conclusions: Reflex testing for 3199del6 should be considered whenever I148T is identified. Reflex testing is of particular importance for any symptomatic patient or whenever one member of a couple carries a deleterious CF mutation and the other member is an I148T heterozygote. Further population data are required to determine if I148T, in the absence of 3199del6, is associated with mild or atypical CF or male infertility.

CONTEXT Bioelectronic sensors, which combine microchip and biological components, are an emerging technology in clinical diagnostic testing. An electronic detection platform using DNA biochip technology (eSensor) is under development for molecular diagnostic applications. Owing to the novelty of these devices, demonstrations of their successful use in practical diagnostic applications are limited. OBJECTIVE To assess the performance of the eSensor bioelectronic method in the validation of 6 Epstein-Barr virus-transformed blood lymphocyte cell lines with clinically important mutations for use as sources of genetic material for positive controls in clinical molecular genetic testing. Two cell lines carry mutations in the CFTR gene (cystic fibrosis), and 4 carry mutations in the HFE gene (hereditary hemochromatosis). DESIGN Samples from each cell line were sent for genotype determination to 6 different molecular genetic testing facilities, including the laboratory developing the DNA biochips. In addition to the bioelectronic method, at least 3 different molecular diagnostic methods were used in the analysis of each cell line. Detailed data were collected from the DNA biochip output, and the genetic results were compared with those obtained using the more established methods. RESULTS We report the successful use of 2 applications of the bioelectronic platform, one for detection of CFTR mutations and the other for detection of HFE mutations. In all cases, the results obtained with the DNA biochip were in concordance with those reported for the other methods. Electronic signal output from the DNA biochips clearly differentiated between mutated and wild-type alleles. This is the first report of the use of the cystic fibrosis detection platform. CONCLUSIONS Bioelectronic sensors for the detection of disease-causing mutations performed well when used in a "real-life" situation, in this case, a validation study of positive control blood lymphocyte cell lines with mutations of public health importance. This study illustrates the practical potential of emerging bioelectronic DNA detection technologies for use in current molecular diagnostic applications.

BACKGROUND:Germ-line truncating mutations in the E-cadherin (CDH1) gene have been found in families with hereditary diffuse gastric cancer. These families are characterized by a highly penetrant susceptibility to diffuse gastric cancer with an autosomal dominant pattern of inheritance, predominantly in young persons. We describe genetic screening, surgical management, and pathological findings in young persons with truncating mutations in CDH1 from two unrelated families with hereditary diffuse gastric cancer.METHODS:Mutation-specific predictive genetic testing was performed by polymerase-chain-reaction amplification, followed by restriction-enzyme digestion and DNA sequencing in Family 1 and by heteroduplex analysis in Family 2. A total gastrectomy was performed prophylactically in five carriers of mutations who were between 22 and 40 years old. In each case, the entire mucosa of the stomach was extensively sampled for microscopical analysis.RESULTS:Superficial infiltrates of malignant signet-ring cells were identified in the surgical samples from all five persons who underwent gastrectomy. These early diffuse gastric cancers were multifocal in three of the five cases, and in one person infiltrates of malignant signet-ring cells were present in 65 of the 140 tissue blocks analyzed, representing in aggregate less than 2 percent of the gastric mucosa.CONCLUSIONS:We recommend genetic counseling and consideration of prophylactic gastrectomy in young, asymptomatic carriers of germ-line truncating CDH1 mutations who belong to families with highly penetrant hereditary diffuse gastric cancer.

More than 850 mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene have been reported to the Cystic Fibrosis (CF) Consortium. A missense mutation, S1235R, was originally reported in a CF patient with a second mutation (G628R) on the same chromosome. The clinical significance of S1235R was not clear. S1235R is not among the commonly reported mutations, and it is not routinely screened for in most laboratories. However, we have identified this variant in our laboratories at a higher frequency than many of the other CF mutations. Among more than 3,000 patients tested for either a possible diagnosis of CF or to determine CF carrier status, we identified 50 patients heterozygous for S1235R. No patients were homozygous for S1235R. The allele frequency of S1235R in this population (∼1%) was higher than that of the G551D or G542X CF mutations. Patients found to carry S1235R ranged in age from 1 day to 73 years. Indications for testing included rule out CF (15 cases), prenatally diagnosed echogenic bowel (2 cases), meconium ileus/obstruction at birth (3 cases), carrier screening with a positive family history (11 cases), carrier screening with a negative family history (17 cases) and unknown (2 cases). Four patients were compound heterozygotes for a second CFTR mutation: 2 cases (one family) were N1303K/S1235R and 2 unrelated cases were AF508/S1235R. Clinical data on those patients will be presented. No patient tested so far (N=31) carried the G628R CFTR mutation. Our data suggests that S1235R, when combined with a second CF mutation, may be pathogenic, although phenotypic manifestations appear to be variable. However, the possibility that this represents a rare polymorphism cannot be discounted completely. Genetic counseling issues are difficult when S1235R is identified, even in the presence of a second known mutation, especially in prenatal cases.

Cationic trypsinogen and cystic fibrosis mutations have been identified in pancreatitis patients, although no study has looked for mutations in both genes in the same patient. Pancreatitis can be induced by alcohol, although not all alcoholics develop pancreatitis. We hypothesize that this phenomenon is due to a genetic predisposition in persons with alcohol-related pancreatitis. We performed sequence analysis of the cationic trypsinogen-coding region in 46 alcohol-related pancreatitis patients and 16 patients with pancreatitis due to causes other than alcohol. We also screened for 40 cystic fibrosis mutations including the 5T allele. No cationic trypsinogen mutations were identified. Cystic fibrosis mutation screening identified the DeltaF508 mutation in two Caucasian alcoholic patients (P<0.025). The cystic fibrosis mutation carrier frequency in African-American alcoholic patients was 3%, which was not significantly increased compared with the normal carrier frequency. The frequency of the 5T allele was not significantly increased compared with the normal population carrier frequency in either racial group. These results may suggest a role for the cystic fibrosis gene in alcohol-related pancreatitis but indicate that cationic trypsinogen mutations are not a common predisposing risk factor for alcohol-related pancreatitis. A multicenter study is necessary to attain sufficient numbers to come to a conclusion.

Previous studies have shown that specific short-tandem-repeat (STR) and single-nucleotide-polymorphism (SNP)-based haplotypes within and among unaffected and fragile X white populations are found to be associated with specific CGG-repeat patterns. It has been hypothesized that these associations result from different mutational mechanisms, possibly influenced by the CGG structure and/or cis-acting factors. Alternatively, haplotype associations may result from the long mutational history of increasing instability. To understand the basis of the mutational process, we examined the CGG-repeat size, three flanking STR markers (DXS548-FRAXAC1-FRAXAC2), and one SNP (ATL1) spanning 150 kb around the CGG repeat in unaffected (n=637) and fragile X (n=63) African American populations and compared them with unaffected (n=721) and fragile X (n=102) white populations. Several important differences were found between the two ethnic groups. First, in contrast to that seen in the white population, no associations were observed among the African American intermediate or "predisposed" alleles (41-60 repeats). Second, two previously undescribed haplotypes accounted for the majority of the African American fragile X population. Third, a putative "protective" haplotype was not found among African Americans, whereas it was found among whites. Fourth, in contrast to that seen in whites, the SNP ATL1 was in linkage equilibrium among African Americans, and it did not add new information to the STR haplotypes. These data indicate that the STR- and SNP-based haplotype associations identified in whites probably reflect the mutational history of the expansion, rather than a mutational mechanism or pathway.

Fetal echogenic bowel has been reported as a normal variant in the second trimester, and has also been associated with an adverse fetal outcome, including cystic fibrosis (CF), an autosomal recessive genetic disease. Previous studies have reported that 3.3 to 13.3 per cent of fetuses with echogenic bowel discovered during the second trimester were affected with CF. Between 1994 and 1998 our laboratory tested 159 cases with echogenic bowel detected during a routine ultrasound examination. The ethnic/racial background of cases included Caucasian, African–American, Middle Eastern, Hispanic, Ashkenazi Jewish and Asian. We identified two CF fetuses (1.3 per cent) and eight fetuses with a single identifiable CF mutation (5 per cent) within this diverse population. These data indicated that the risk of CF in a fetus with echogenic bowel in this population was less than the 3.3 to 13.3 per cent prior risk currently used in most Bayesian calculations. Furthermore, the results suggested that specific risks for couples should be calculated using data specific for their ethnic or racial background. Based on our results, we recommend either amniocentesis for fetal CF studies or CF carrier screening of both parents when fetal echogenic bowel is detected as a 1.3 per cent risk of CF is considered high enough to warrant further testing. Copyright © 1999 John Wiley & Sons, Ltd.

Hereditary pancreatitis (HP) is a rare, early-onset autosomal dominant genetic disorder characterized by epigastric pain and often more serious complications. Mutations have been identified in the cationic trypsinogen gene in patients with HP and in the cystic fibrosis transmembrane regulator (CFTR) gene in patients with HP and chronic pancreatitis. Pancreatitis can be induced by exposure to certain environmental factors, such as alcohol, although not all persons exposed will develop symptoms of the disease. We hypothesized that this phenomenon is due to a genetic predisposition in persons with pancreatitis attributed to alcohol abuse. We obtained informed written consent for participation in this study. We collected blood samples from 64 patients with a discharge diagnosis of pancreatitis. Review of the medical record and patient interviews were used to ascertain the phenotype, etiology of pancreatitis and to determine whether there was a family history of pancreatitis. Forty-six patients (34 African American, 11 Caucasian and I Hispanic) had either alcohol-induced pancreatitis or had pancreatitis and a history of alcohol abuse. 6 patients (13%) reported a family history of pancreatitis in at least one first-degree relative. Sequence analysis for the 5 exons and flanking intronic sequences of the cationic trypsinogen gene identified several unreported intronic polymorphisms which are most likely of no clinical significance but did not identify any novel or previously reported mutations. We screened for 39 CF mutations which account for approximately 90% of CF mutations in individuals of Northern European descent and 67% of African American mutations. The ΔF508 CF mutation was identified in 2 Caucasian patients (18%) and a previously unreported missense mutation in exon 19 of the CFTR was identified in an African American patient (3%). The significance of this novel mutation with respect to CFTR function is not known. The carrier frequency for CF mutations is 4% for Caucasians and 1.4% for African Americans. Analysis of the CFTR “5T” allele is in progress. Although our sample size is small, these results suggest that screening for cationic trypsinogen mutations will not be useful in identifying patients with alcohol-related pancreatitis. However, because the carrier frequency for CF mutations in patients with pancreatitis and alcoholism is increased above the population carrier frequency, these studies suggest a possible role of the CFTR in alcohol-related pancreatitis.

Homozygosity for the mutation Cys282Tyr in the HFE gene has recently been identified as a cause of hereditary hemochromatosis, a disorder resulting in the inappropriate absorption of iron. Approximately 10% of Caucasians are heterozygous for this mutation; however, the gene frequency in African Americans is unknown. A study of a control population of African Americans was performed to determine the frequency of the Cys282Tyr and His63Asp alleles in this ethnic group. The carrier frequency for each mutant allele in our African American population was 3.0%. DNA studies of four African-American hemochromatosis patients did not identify any individuals with the Cys282Tyr allele. These findings suggest that if the Cys282Tyr mutation confers susceptibility to hemochromatosis in Caucasians (as suggested by recent studies) there is an alternative mechanism for hemochromatosis in the American black population. Am. J. Hematol. 58:213–217, 1998. © 1998 Wiley-Liss, Inc.

The most commonly reported manifestations of 16q deletions are severe growth and developmental disorders and anomalies of the craniofacial, visceral, and musculoskeletal systems. We reviewed the findings of patients reported with 16q- syndrome and compared them to our patient, a 4 1/2-year-old boy with a deletion of 16q23.1. Findings include psychomotor retardation, hypotonia, high forehead, hypertelorism, upslanting palpebral fissures, low-set abnormally modeled ears, and talipes equinovarus. Anomalies present in our patient not reported in others with 16q- syndrome include bilateral cataracts, iris coloboma, and autistic-like behavior. It is of note that a locus for autosomal dominant congenital cataract, known as Marner cataract, was mapped previously to 16q22. Because our patient has bilateral cataracts and a unilateral iris coloboma, it seems likely that a gene involved in ocular development is located within 16q23.1. Our patient's deletion may also include the gene involved in Marner cataract and may further assist in the isolation of this gene.