Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems.

We describe here the design and initial implementation of the eMERGE-PGx project. eMERGE-PGx, a partnership of the Electronic Medical Records and Genomics Network and the Pharmacogenomics Research Network, has three objectives: (i) to deploy PGRNseq, a next-generation sequencing platform assessing sequence variation in 84 proposed pharmacogenes, in nearly 9,000 patients likely to be prescribed drugs of interest in a 1- to 3-year time frame across several clinical sites; (ii) to integrate well-established clinically validated pharmacogenetic genotypes into the electronic health record with associated clinical decision support and to assess process and clinical outcomes of implementation; and (iii) to develop a repository of pharmacogenetic variants of unknown significance linked to a repository of electronic health record-based clinical phenotype data for ongoing pharmacogenomics discovery. We describe site-specific project implementation and anticipated products, including genetic variant and phenotype data repositories, novel variant association studies, clinical decision support modules, clinical and process outcomes, approaches to managing incidental findings, and patient and clinician education methods.

Fryns syndrome phenotype caused by chromosome microdeletions at 15q26.2 and 8p23.1.

BACKGROUND: Fryns syndrome (FS) is the commonest autosomal recessive syndrome in which congenital diaphragmatic hernia (CDH) is a cardinal feature. It has been estimated that 10% of patients with CDH have FS. The autosomal recessive inheritance in FS contrasts with the sporadic inheritance for the majority of patients with CDH and renders the correct diagnosis critical for accurate genetic counselling. The cause of FS is unknown. METHODS: We have used array comparative genomic hybridisation (array CGH) to screen patients who have CDH and additional phenotypic anomalies consistent with FS for cryptic chromosome aberrations. RESULTS: We present three probands who were previously diagnosed with FS who had submicroscopic chromosome deletions detected by array CGH after normal karyotyping with G-banded chromosome analysis. Two female infants were found to have microdeletions involving chromosome band 15q26.2 and one male had a deletion of chromosome band 8p23.1. CONCLUSIONS: We conclude that phenotypes similar to FS can be caused by submicroscopic chromosome deletions and that high resolution karyotyping, including array CGH if possible, should be performed prior to the diagnosis of FS to provide an accurate recurrence risk in patients with CDH and physical anomalies consistent with FS.

Ring X and other structural X chromosome abnormalities: X inactivation and phenotype.

Patients who carry a structural abnormality of the X chromosome are a fascinating group who have provided opportunities to evaluate genotype/phenotype correlation in relation to X chromosome content and inactivation. Turner syndrome (TS) is most commonly associated with a 45,X karyotype and presents with an array of phenotypes, the main ones being poor viability in utero, ovarian failure and infertility, short stature, lymphedema, and other congenital malformations but usually not mental retardation. In some TS patients the karyotype shows both a normal X and a structurally rearranged X chromosome. These structural abnormalities, which include deletions, duplications, inversions, translocations, and rings, are associated with chromosome breaks and significant imbalance of gene content of the X chromosome. However, such abnormalities are generally well tolerated because of the preferential inactivation of the abnormal X, which can restore, at least in part, a balanced genetic makeup. This beneficial effect of X inactivation results in a mild phenotype in most patients with structural abnormalities of the X, similar to that found in TS patients with a 45,X karyotype. However, in cases of ring X chromosomes and of X/autosome translocations the incidence of mental retardation and other congenital abnormalities can be significantly higher than in TS. These abnormal phenotypes can be ascribed to failed or partial X inactivation and/or incomplete selection in favor of cells with normal balance of gene expression. In this article, we present phenotype/genotype correlation in female patients with structural abnormalities of the X and address the role of X inactivation and cell selection in the phenotypic findings. Our review emphasizes a subset of rare patients with ring X chromosomes who have provided evidence of a direct role for X inactivation in determining phenotypes.

Familial cryptic (20;21) translocation identified by in situ hybridization technologies.

We report on a familial cryptic (20;21) translocation [(t20;21)] that was initially suspected with the observation of a single chromosome 21 specific signal in an interphase nuclei by in situ hybridization (FISH) study performed on a 34-week gestation amniotic fluid specimen. The genetic amniocentesis was prompted by the presence of fetal anomalies detected by ultrasound. In addition, there was a family history of a maternal uncle with mental retardation and multiple malformations and an apparently normal karyotype. No obvious aberration could be detected in the G-banded karyotype prepared from the amniotic fluid specimen. A FISH study using a chromosome 21 specific long arm probe and chromosome 20 whole chromosome paint, however, showed an unbalanced rearrangement in the fetus [46,XY, der(21)t(20;21)(q13.2;q22.13 or 22.2) mat]. The mother and maternal grandmother were demonstrated to be balanced translocation carriers. These results were confirmed by multicolor karyotyping. This familial aberration was discovered by chance in the interphase FISH analysis. Our experience with this case, however, serves to emphasize the importance of the reevaluation of patients with mental retardation and congenital malformations of unknown cause and prudent use of multicolor karyotyping in the detection of cryptic cytogenetic rearrangements.

Brachydactyly type A1 with abnormal menisci and scoliosis in three generations.

We report a three-generation family in which four members had brachydactyly type A1, degenerative arthritis of the knee as a complication of abnormal menisci, and variable scoliosis. Nine of the 15 individuals in the two generations preceding the proband had brachydactyly. Three of these nine had degenerative arthritis of the knee including the proband's father who had meniscal degeneration with tears. One other had radiologically confirmed discoid menisci. Of those with brachydactyly, five also had scoliosis. Although autosomal dominant inheritance of brachydactyly A1 and discoid menisci have been reported separately, cosegregation of these features in one family has not previously been described and seems to comprise a unique autosomal dominant condition. The combination of brachydactyly, meniscal abnormalities including discoid meniscus, and scoliosis suggests that this disorder represents a new osteochondrodysplasia syndrome.

Familial neurofibromatosis 1 microdeletions: cosegregation with distinct facial phenotype and early onset of cutaneous neurofibromata.

A notable subset of the recent literature on the disorder neurofibromatosis type 1 (NF1) describes patients with NF1, facial anomalies, and other unusual findings. We describe a molecular re-evaluation of two such families reported previously by Kaplan and Rosenblatt [1985], who suggested that their NF1 manifestations, facial phenotype, and other findings could result from a disorder distinct from NF1. Submicroscopic deletions involving the NF1 gene were identified in both families by fluorescent in situ hybridization and analysis of somatic cell hybrids. Affected subjects of the first family were heterozygous for a microdeletion of approximately 2 Mb, which included the entire NF1 gene and flanking contiguous sequences. The family was remarkable for cosegregation of the NF1 microdeletion with facial abnormalities and a pattern of early onset of cutaneous neurofibromata upon transmission from an affected mother to her three affected children. The propositus of the second family carried a deletion that at the least involved NF1 exon 2 through intron 27, which is > 200 kilobases in length. Because all persons in the family were deceased, the size of the deletion could not be determined precisely. Facial anomalies were observed in the propositus and his NF1-affected mother and sister. The data from these families support our hypothesis, which was initially based solely on sporadic deletion cases, that deletion of the entire NF1 gene, or in conjunction with deletion of unknown contiguous genes, causes the facial anomalies and early onset of neurofibromata observed in this subset of NF1 patients. In addition, other features observed in the persons in these families suggest that some NF1 microdeletion patients may be at increased risk for connective tissue abnormalities and/or neoplasms.

Trisomy 10p: report of an unusual mechanism of formation and critical evaluation of the clinical phenotype.

A de novo tandem inverted duplication of 10p was diagnosed in a 17-week fetus. The appearance of GTG banded preparations and the results of fluorescence in situ hybridization (FISH) studies are consistent with duplication of the entire arm, including the telomere. The FISH studies also demonstrated the presence of chromosome 10 alphoid repeats at the junction between the inverted segment and the long arm, consistent with the presence of the entire long arm of the abnormal chromosome. Therefore, this is a case of pure trisomy 10p without an associated deficiency of any other chromosome segment. A comparison of the phenotype associated with pure trisomy 10p and trisomy associated with a duplication/deficiency state documented a higher frequency (of borderline significance) of clubfoot and high-arched/cleft palate in the cases of pure trisomy. The frequency of palatal anomalies was observed to be significantly higher in the cases where the breakpoint of the trisomic segment is in the most proximal band (10p11). However, other clinical manifestations were observed inconsistently, even in the cases with pure, nearly complete trisomy 10p. Therefore, a clearly defined trisomy 10p clinical syndrome could not be documented in this study.

The detection of contiguous gene deletions at the neurofibromatosis 1 locus with fluorescence in situ hybridization.

Neurofibromatosis type 1 (NF1) is a common genetic disorder characterized primarily by the development of multiple neurofibromas and pigmentary changes. The recent identification of contiguous gene deletions in NF1, a previously unrecognized molecular basis for this disorder, raises important questions regarding deletion frequency in the patient population and the role that contiguous genes may play in the physical manifestations of NF1 patients. To facilitate the identification of patients with large NF1 deletions, we have isolated clones carrying large genomic segments from the NF1 locus and tested their efficacy as probes for fluorescence in situ hybridization (FISH). Clone P1-9 spans approximately 65 kb of the NF1 gene, including exons 2-11, and clone P1-12 carries approximately 55 kb of NF1 intron 27B. FISH studies performed with P1-9, P1-12, and a set of overlapping 1F10 cosmid clones mapping telomeric to the NF1 locus identified large deletions in two new neurofibromatosis type 1 patients who, like previously characterized deletion patients, had mildly dysmorphic facial features and large numbers of cutaneous neurofibromas.

Smooth muscle tumors associated with X-linked Alport syndrome: carrier detection in females.

X-linked Alport syndrome (AS) associated with diffuse esophageal leiomyomatosis (DL) has been reported to be due to deletions removing the 5' ends of both the COL4A5 and COL4A6 genes, encoding the alpha 5 and alpha 6 chains of type IV collagen, respectively, whereas a variety of mutations in COL4A5 has been identified in patients with AS alone. Here we report three additional DL-AS patients who also display deletions removing the 5' ends of both COL4A5 and COL4A6 genes. Furthermore, we tracked the mutation in 15 females belonging to six DL-AS families by gene copy number determination. We found that, like AS, DL is transmitted as an X-linked dominant trait but, contrary to AS, DL is fully penetrant and completely expressed in females. These results are in agreement with our previous work suggesting that DL could be due to a dominant effect of an abnormal alpha 6 (IV) collagen chain. Finally, we have detected a similar deletion of the COL4A5 and COl4A6 genes in a DL affected female who showed no sign of nephropathy, demonstrating the AS carrier status of this DL patient. These results emphasize the importance of molecular analysis of female DL patients for genetic counseling.

Deletions of both alpha 5(IV) and alpha 6(IV) collagen genes in Alport syndrome and in Alport syndrome associated with smooth muscle tumours.

Diffuse oesophageal leiomyomatosis (DL), an inherited smooth muscle proliferation process, has been reported to be associated with Alport syndrome (AS), a familial nephropathy, mainly dominant X-linked inherited, and characterized by ultrastructural changes of the glomerular basement membrane. The COL4A5 gene, encoding the alpha 5 chain of type IV collagen, has been identified as the site of mutations in families with X-linked AS. Recently, a novel alpha 6(IV) collagen chain encoding gene has been mapped closely upstream of COL4A5, and disruption of the 5' end of both genes has been reported in four patients with DL and AS (DL-AS). Here, we report a long-range restriction map around the COL4A6 locus, and show that the COL4A5/COL4A6 deletion observed in seven patients with DL-AS encompasses only the two first exons of COL4A6, with a breakpoint located in the second intron of COL4A6, whose size exceeds 65 kb. Furthermore, we demonstrate that three patients with AS without DL, known to have a deletion of the 5' part of the COL4A5 gene, display a larger deletion in COL4A6. Moreover, a COL4A6 mRNA product was detected by reverse-transcription-polymerase chain reaction in an oesophageal tumour sample of a patient with DL-AS. These results suggest that DL-AS could be caused by an abnormal truncated alpha 6(IV) chain.

Cytotoxicity mediated by conditional expression of a carboxyl-terminal derivative of the beta-amyloid precursor protein.

The beta amyloid peptide which accumulates within the brains of patients with Alzheimer's disease (AD) is proteolytically derived from a precursor protein (beta PP). We established and characterized four stably transformed human neuroblastoma cell lines which conditionally expressed a partial beta PP fusion protein (amino-17 residues+carboxyl-99 residues; S beta C). Conditional expression of S beta C was achieved using a tetracycline-responsive promoter system. Expression of this fusion protein in one of the cell lines resulted in pronounced cytotoxicity. Addition of n6,O2'-dibutyryl adenosine 3',5'-cyclic monophosphate and/or fetal bovine serum to the culture medium of this cell line further elevated the level of S beta C expression and enhanced the associated cytotoxicity. Conditioned medium, acquired from cells expressing S beta C, was not cytotoxic. These findings suggest that modulation of beta PP expression and/or metabolism can have cytotoxic consequences. This is the first report of cytotoxic effects mediated by conditional expression of a beta PP derivative. This immortal cell line provides a unique opportunity to screen for complementary DNAs which suppress this toxicity. Such cDNAs could help elucidate the processes underlying S beta C mediated cytotoxicity which in turn could further our understanding of the pathogenesis of AD and could also provide additional candidate genes for various forms of familial AD.

Use of yeast artificial chromosomes (YACs) for studying control of gene expression: correct regulation of the genes of a human beta-globin locus YAC following transfer to mouse erythroleukemia cell lines.

We demonstrate that transfer of a yeast artificial chromosome (YAC) containing 230 kb of the human beta-globin locus into mouse erythroleukemia cells by fusion results in correct developmental regulation of the human beta-like globin genes. Additionally, we show that early after hybrid formation, human embryonic epsilon- and fetal gamma-globin genes are coexpressed with the adult beta gene but that after 10-20 weeks in culture, globin gene expression switches to predominantly adult. Thus, in contrast to shorter gene constructs, the globin genes of the beta-globin locus YAC are regulated like the chromosomal globin genes. These results indicate that transfer of YACs into established cell lines can be used for the analysis of the developmental control of multigenic and developmentally regulated human loci.

Cloning of the human homolog of the CDC34 cell cycle gene by complementation in yeast.

In a screen designed to isolate human cDNAs that complement a yeast G2 phase checkpoint mutation (mec1), we isolated a cDNA homologous to the Saccharomyces cerevisiae CDC34 gene. The human CDC34 cDNA can functionally substitute for the yeast CDC34 gene and represents a mammalian homolog of the group of yeast genes required for the late G1-->S phase transition. The human CDC34 gene is expressed in multiple cell lines as a unique species and Southern blot analysis reveals evidence for a single gene that is highly conserved in higher eukaryotes. The human gene is located on the far telomeric region of 19p13.3 in a location that defines a region of homology between human chromosome 19p and mouse chromosome 11.

Phenotypic correlations of ocular coloboma without known cause.

Ocular coloboma can occur as an autosomal dominant condition or as part of a known syndrome or chromosomal abnormality. We have designated those patients with ocular coloboma who do not fit into any of these three groups as having coloboma without known cause. We completed a retrospective review of 58 patients from our clinics with coloboma without known cause to determine the frequency of other co-existing congenital malformations and mental retardation. Mental retardation was present in 14 of the 42 patients (33%) who were more than 1 year of age. However, only 14% of the children who had no other malformations had mental retardation, whereas 57% of those with other malformations were mentally retarded. We found that the severity of the colobomatous malformation did not correlate with intellect.

Mapping of the distal boundary of the X-inactivation center in a rearranged X chromosome from a female expressing XIST.

A female patient with primary amenorrhea, immature secondary sexual characteristics, and tall stature was found to have a normal X chromosome and a rearranged X [rea(X)] chromosome that resembled an 'isochromosome' Xp, but retained the proximal portion of Xq. The rea(X) was interpreted as rec(X)dup p,inv(X)(p11.4q13). Replication studies demonstrated that the rea(X) was always the late-replicating and, therefore, presumably inactive X chromosome, which must contain the X-inactivation center. Consistent with this interpretation, fluorescence in situ hybridization demonstrated that the rea(X) retained the XIST gene, and reverse transcription polymerase chain reaction analysis showed that XIST was expressed in the patient's cells. By fluorescence in situ hybridization with previously mapped probes, the breakpoint of the rea(X) was located within an approximately 500-kb region located approximately 200 to 700 kb distal to the XIST locus. This is the closest breakpoint distal to XIST in an inactivated X chromosome and, therefore, defines a new distal boundary for the X-inactivation center in humans.

DNA deletion associated with hereditary neuropathy with liability to pressure palsies.

Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant disorder that causes episodes of focal demyelinating neuropathy following minor trauma to peripheral nerves. We assign the HNPP locus to chromosome 17p11.2 and demonstrate the presence of a large interstitial deletion associated with this disorder in three unrelated pedigrees. De novo deletion is documented in one pedigree. The deleted region appears uniform in all pedigrees and includes the gene for peripheral myelin protein 22 (PMP-22), suggesting that underexpression of PMP-22 may cause HNPP. The deletion in HNPP spans approximately 1.5 Mb and includes all markers that are known to map within the Charcot-Marie-Tooth neuropathy type 1A (CMT1A) duplication. Furthermore, the breakpoints in HNPP and CMT1A map to the same intervals in 17p11.2, suggesting that these genetic disorders may be the result of reciprocal products of unequal crossover.

Predictive value of minor anomalies: II. Use in cohort studies to identify teratogens.

Cohort studies of putative human teratogens can identify the full spectrum of phenotypic effects, including both major malformations and minor anomalies. Cohort studies which include the much more common minor anomalies make it possible to use a relatively small number of exposed and unexposed infants to identify an increase in the frequency of malformations. We evaluated this use of minor anomalies in a cohort study of newborn infants who had been exposed in utero to three putative teratogens: insulin-dependent diabetes mellitus in the mother and the use of the anticonvulsant phenytoin and exogenous sex hormones by the mother. In addition, the reproducibility of identifying minor anomalies was tested by comparing the results of examinations by two independent observers of 444 unexposed infants. The frequency of minor anomalies was increased among infants of diabetic mothers. However, the reproducibility of identifying minor anomalies was poor. We conclude that the examination of teratogen-exposed infants for minor anomalies cannot be used in epidemiologic studies of putative teratogens unless special efforts are made to maximize consistency in the identification of these features.

Predictive value of minor anomalies. I. Association with major malformations.

We examined 4305 white newborn infants for 114 minor physical features and major malformations to evaluate the hypothesis that the presence of three or more minor anomalies is highly predictive of a major malformation. We confirmed that the infant with three or more minor anomalies is at increased risk for a major malformation. However, this risk (19.6%) was much lower than the risk of 90% popularized by Smith and based on the study of Marden et al. (J Pediatr 1964;64:357). Analysis of the findings in the two studies showed that the lower predictive value was probably related to differences in study design. Nevertheless, some minor anomalies remain essential to the early recognition of several serious malformation syndromes.