Exome and genome sequencing: a revolution for the discovery and diagnosis of monogenic disorders.

Massively parallel DNA sequencing has revolutionized analyses of human genetic variation. From having been out of reach for individual research groups and even more so for clinical diagnostic laboratories until recently, it is now possible to analyse complete human genomes within reasonable time frames and at a reasonable cost using technologies that are becoming increasingly available. This represents a huge advance in our ability to provide correct diagnoses for patients with rare inherited disorders and their families. This paradigm shift is especially dramatic within the area of monogenic disorders. Not only can rapid and safe diagnostics of virtually all known single-gene defects now be established, but novel causes of disease in previously unsolved cases can also be identified, illuminating novel pathways important for normal physiology. This greatly increases the capability not only to improve management of rare disorders, but also to improve understanding of pathogenetic mechanisms relevant for common, complex diseases.

Identification of a duplication within the GDF9 gene and novel candidate genes for primary ovarian insufficiency (POI) by a customized high-resolution array comparative genomic hybridization platform.

STUDY QUESTION: Can high-resolution array comparative genomic hybridization (CGH) analysis of DNA samples from women with primary ovarian insufficiency (POI) improve the diagnosis of the condition and identify novel candidate genes for POI? SUMMARY ANSWER: A mutation affecting the regulatory region of growth differentiation factor 9 (GDF9) was identified for the first time together with several novel candidate genes for POI. WHAT IS KNOWN ALREADY: Most patients with POI do not receive a molecular diagnosis despite a significant genetic component in the pathogenesis. STUDY DESIGN, SIZE, DURATION: We performed a case-control study. Twenty-six patients were analyzed by array CGH for identification of copy number variants. Novel changes were investigated in 95 controls and in a separate population of 28 additional patients with POI. The experimental procedures were performed during a 1-year period. PARTICIPANTS/MATERIALS, SETTING, METHODS: DNA samples from 26 patients with POI were analyzed by a customized 1M array-CGH platform with whole genome coverage and probe enrichment targeting 78 genes in sex development. By PCR amplification and sequencing, the breakpoint of an identified partial GDF9 gene duplication was characterized. A multiplex ligation-dependent probe amplification (MLPA) probe set for specific identification of deletions/duplications affecting GDF9 was developed. An MLPA probe set for the identification of additional cases or controls carrying novel candidate regions identified by array-CGH was developed. Sequencing of three candidate genes was performed. MAIN RESULTS AND THE ROLE OF CHANCE: Eleven unique copy number changes were identified in a total of 11 patients, including a tandem duplication of 475 bp, containing part of the GDF9 gene promoter region. The duplicated region contains three NOBOX-binding elements and an E-box, important for GDF9 gene regulation. This aberration is likely causative of POI. Fifty-four patients were investigated for copy number changes within GDF9, but no additional cases were found. Ten aberrations constituting novel candidate regions were detected, including a second DNAH6 deletion in a patient with POI. Other identified candidate genes were TSPYL6, SMARCC1, CSPG5 and ZFR2. LIMITATIONS, REASONS FOR CAUTION: This is a descriptive study and no functional experiments were performed. WIDER IMPLICATIONS OF THE FINDINGS: The study illustrates the importance of analyzing small copy number changes in addition to sequence alterations in the genetic investigation of patients with POI. Also, promoter regions should be included in the investigation. STUDY FUNDING/COMPETING INTERESTS: The study was supported by grants from the Swedish Research council (project no 12198 to A.W. and project no 20324 to A.L.H.), Stockholm County Council (E.I., A.W. and K.R.W.), Foundation Frimurare Barnhuset (A.N., A.W. and M.B.), Karolinska Institutet (A.N., A.L.H., E.I., A.W. and M.B.), Novo Nordic Foundation (A.W.) and Svenska Läkaresällskapet (M.B.). The funding sources had no involvement in the design or analysis of the study. The authors have no competing interests to declare. TRIAL REGISTRATION NUMBER: Not applicable.

A sequence variation in 3'UTR of CYP21A2 gene correlates with a mild form of congenital adrenal hyperplasia.

BACKGROUND: Congenital adrenal hyperplasia (CAH) is mainly caused by the deficiency of the 21-hydroxylase enzyme coded by the CYP21A2 gene. However, some alleles in the non-classical form (NC-CAH) remain without identified mutations, suggesting the involvement of regulatory regions. AIM: Our objective was to study an allele carrying the variant *13 G>A in the 3'UTR of the CYP21A2 gene identified in some patients with a mild form of NC-CAH in order to verify the possible implication of this variation with the phenotype observed. SUBJECTS AND METHODS: Among all the subjects in whom the CYP21A2 gene was analyzed, 14 patients and 7 relatives heterozygous or homozygous for the *13 G>A substitution in 3'UTR were selected. Sequencing of DNA, genotyping, multiplex ligation-dependent probe amplification (MLPA), in vitro studies and bioinformatic analysis were performed. RESULTS: The haplotype of the *13 G>A allele was identical in all the subjects with a monomodular structure composed by one C4A gene and one CYP21A2 gene without a second module with the CYP21A1P pseudogene. No other concomitant mutations were found in the region extending from 3 kb in the promoter and encompassing the polyadenylation signal. Both bioinformatic analysis and in vitro studies predicted an alteration of the RNA folding and expression, but no miRNA target sequences were found in this region. CONCLUSIONS: The identification of a substitution in the 3'UTR of the gene associated with a mild form of NC-CAH suggests the importance of analyzing the CYP21A2 untranslated regions to better characterize and treat this subgroup of patients.

Inhibition of CYP21A2 enzyme activity caused by novel missense mutations identified in Brazilian and Scandinavian patients.

BACKGROUND: Most patients with 21-hydroxylase deficiency carry CYP21A1P-derived mutations, but an increasing number of novel and rare mutations have been reported in disease-causing alleles. OBJECTIVE: Functional effects of three novel (p.G56R, p.L107R, p.L142P) and one recurrent (p.R408C) CYP21A2 mutations were investigated. The degree of enzyme impairment caused by p.H62L alone or combined to p.P453S was also analyzed. DESIGN: The study included 10 Brazilian and two Scandinavian patients. To determine the deleterious role of each mutant protein, in vitro assays were performed in transiently transfected COS-1 cells. For a correct genotype-phenotype correlation, the enzymatic activities were evaluated toward the two natural substrates, 17-hydroxyprogesterone and progesterone. RESULTS: Low levels of residual activities obtained for p.G56R, p.L107R, p.L142P, and p.R408C mutants classified them as classical congenital adrenal hyperplasia mutations, whereas the p.H62L showed an activity within the range of nonclassical mutations. Apparent kinetic constants for p.H62L confirmed the nonclassical classification as the substrate binding capacity was within the same magnitude for mutant and normal enzymes. A synergistic effect was observed for the allele bearing the p.H62L+p.P453S combination because it caused a significant reduction in the enzymatic activity. CONCLUSIONS: We describe the functional analysis of five rare missense mutations identified in Brazilian and Scandinavian patients. The p.G56R, p.L107R, and p.L142P are reported for the first time. Most probably these novel mutations are closer to null than the p.I172N, but for the p.G56R, that might not be the case, and the p.H62L is definitely a nonclassical mutation.

Gene dosage imbalances in patients with 46,XY gonadal DSD detected by an in-house-designed synthetic probe set for multiplex ligation-dependent probe amplification analysis.

The development of a testis requires the proper spatiotemporal expression of the SRY gene and other genes that act in a dosage-sensitive manner. Mutations in the SRY gene account for only 10-15% of patients with 46,XY gonadal disorder of sex development (DSD). To enable the diagnostics of deletions and duplications of genes known to be involved in different forms of DSD, we developed a synthetic probe set for multiplex ligation-dependent probe amplification (MLPA) analysis. Here, we report the results from the analysis of 22 patients with 46,XY gonadal DSD. The analysis with the DSD probe set has led to the identification of two copy number variations, an 800-kb NR0B1 (DAX1) locus duplication on Xp21 in a patient with isolated partial gonadal dysgenesis and a duplication of the SRD5A2 gene that represents a rare normal variant. The described MLPA kit represents an optimal complement to DNA sequence analysis in patients with DSD, enabling screening for deletions and duplications of several genes simultaneously. Furthermore, the second identification of an NR0B1 locus duplication in a patient with isolated gonadal dysgenesis, without dysmorphic features and/or mental retardation, highlights the importance of evaluating NR0B1 duplication in patients with gonadal dysgenesis.

Functional studies of two novel and two rare mutations in the 21-hydroxylase gene.

Congenital adrenal hyperplasia (CAH) is most commonly due to 21-hydroxylase deficiency and presents with a wide spectrum of clinical manifestations, from prenatal virilization and salt-wasting in the neonatal period to precocious pubarche and late-onset hyperandrogenic symptoms during adulthood. A limited number of mutations account for the majority of all mutated alleles, but a growing number of rare mutations are responsible for the disease in some patients. By sequence analysis of the CYP21A2 gene, we identified two novel (I171N and L446P) and two rare (R341P and R426H) mutations in seven Italian patients with CAH. One of the patients was diagnosed with mild non-classical CAH and was found to be a compound heterozygote (I171N/V281L), while all other patients showed severe phenotypes with latent or manifest salt-wasting. The residual activities measured after expression of the four mutant enzymes in COS-1 cells were all below 1% towards both natural substrates (17-OH-progesterone and progesterone) compared with the wild-type protein. All four mutations are, thus, associated with severe enzyme deficiency and are predicted to cause classic CAH if found in trans with other mutations causing severe enzyme deficiency.

CYP21 mutations in simple virilizing congenital adrenal hyperplasia.

We studied the functional and structural effects of two unique missense mutations in CYP21 found in patients with simple virilizing congenital adrenal hyperplasia. The rare variants L300F and V281G were found in two girls who were each hemizygous for one of the mutations. Functional analysis after expression in COS-1 cells revealed that the mutant enzymes had reduced enzymatic activity for conversion of both 17-hydroxyprogesterone (L300F 9.5%, V281G 3.9% of normal) and progesterone (L300F 4.4%, V281G 3.9% of normal). Both mutant enzymes had an increased degradation in mammalian COS-1 cells compared to the normal protein, although the L300F variant affected the degradation pattern to a greater extent. Our data indicate that the residue L300 is important in maintaining normal structure of the 21-hydroxylase enzyme whereas mutations affecting V281 most likely cause impaired enzyme activity by interfering with a specific function(s) of the protein.

Synergistic effect of partially inactivating mutations in steroid 21-hydroxylase deficiency.

Lesions in the gene encoding steroid 21-hydroxylase result in congenital adrenal hyperplasia, with impaired secretion of cortisol and aldosterone from the adrenal cortex and overproduction of androgens. Mild forms of the disease cause late-onset symptoms of hyperandrogenism and are thought to be largely underdiagnosed. A limited number of mutations account for the majority of mutated alleles, but additional rare mutations are responsible for the symptoms in some patients. We previously reported a rare allele in two siblings with late-onset disease. This allele contained three sequence alterations, a C to T transition 4 bases upstream of translation initiation, a CCG to CTG change at codon 105 (P105L), and a CCC to TCC transition at codon 453 (P453S). The latter mutation has been found in other ethnic groups, whereas P105L seems to be unique to this family. We have now analyzed the functional consequences of the -4, P105L, and P453S sequence alterations by in vitro translation and after expression of mutant enzyme in cultured cells. As expected, the base substitution at position-4 had no measurable effect on gene expression. The P105L mutation reduced enzyme activity to 62% for 17-hydroxyprogesterone and 64% for progesterone, and the P453S mutation reduced activity to 68% and 46%, respectively. When present in combination, the two mutations caused a reduction of enzyme activity to 10% for 17-hydroxyprogesterone and 7% for progesterone. These results indicate that P105L and P453S can be expected to result in a very subtle disease manifestation when not found in combination, motivating their inclusion when genotyping to ascertain undiagnosed patients with the mildest forms of 21-hydroxylase deficiency.

Failure of cortisone acetate treatment in congenital adrenal hyperplasia because of defective 11beta-hydroxysteroid dehydrogenase reductase activity.

Congenital adrenal hyperplasia in children is often treated with cortisone acetate and fludrocortisone. It is known that certain patients with congenital adrenal hyperplasia require very high substitution doses of cortisone acetate, and a few patients do not respond to this treatment at all. A patient with 21-hydroxylase deficiency, for whom elevated pregnanetriol (P3) levels in urine were not suppressed during treatment with cortisone acetate (65 mg/m2 x day), was examined. The activation of cortisone to cortisol was assessed by measuring urinary metabolites of cortisone and cortisol. The patient's inability to respond to treatment with cortisone acetate was found to be caused by a low conversion of cortisone to cortisol, assumed to be secondary to low 11beta-hydroxysteroid dehydrogenase activity (11-oxoreductase deficiency). All exons and exon/intron junctions of the 11beta-hydroxysteroid dehydrogenase type1 gene (HSD11L) were sequenced without finding any mutations, but a genetic lesion in the promoter or other regulatory regions cannot be ruled out. The deficient 11-oxoreductase activity seems to have been congenital, in this case, but can possibly be attributable to a down-regulation of the enzyme activity. The results support the use of hydrocortisone, rather than cortisone acetate, for substitution therapy in adrenal insufficiency.

Mutational spectrum of the steroid 21-hydroxylase gene in Sweden: implications for genetic diagnosis and association with disease manifestation.

We have characterized the disease-causing mutations in the steroid 21-hydroxylase genes of 127 patients with different clinical forms of congenital adrenal hyperplasia, representing 186 unrelated chromosomes. The gene was completely absent on 29.8% of the chromosomes, and this together with the I2 splice (27.7%), I173N (20.8%), V282L (5.4%), and R357W (3.8%) mutations constitute 87.5% of all affected chromosomes. In total, 15 different sequence aberrations combine to form 19 different disease-causing alleles. The results confirm that genotyping is an efficient means of diagnosing steroid 21-hydroxylase deficiency, although special consideration is needed to resolve genotypes when full families are not available. Clinical presentations of the different combinations of mutations indicate that genotyping is reliable for prediction of clinical outcome in patients with 21-hydroxylase deficiency. It is especially helpful in determining whether in utero treatment of affected females is indicated and in classifying the severity of 21-hydroxylase deficiency in children diagnosed through neonatal screening, before symptoms have appeared.

Genotyping is a valuable diagnostic complement to neonatal screening for congenital adrenal hyperplasia due to steroid 21-hydroxylase deficiency.

To evaluate genotyping as a diagnostic complement to neonatal screening for congenital adrenal hyperplasia, 91 children who had been diagnosed with this condition between 1986 and 1997 were analyzed for mutations in the steroid 21-hydroxylase gene. Screening levels of 17-hydroxyprogesterone were compared in patients representing different genotypes. Genotyping was performed using allele-specific PCR, the patients were divided into four groups according to the severity of their mutations, and screening results were compared between these groups as well as with 141 values representing false positive samples. The screening levels of 17-hydroxyprogesterone were significantly different in the five groups of samples. Values above 500 nmol/L were clearly associated with the most severe genotypes, whereas conclusions concerning disease severity could not be drawn from individual samples representing lower levels. For example, values around 150-200 nmol/L could be seen in children with all degrees of disease severity and could also constitute false positive samples. We conclude that genotyping is a valuable diagnostic tool and a good complement to neonatal screening, especially in confirming or discarding the diagnosis in cases with slightly elevated 17-hydroxyprogesterone levels. An additional benefit is that it provides information on disease severity, which reduces the risk of overtreatment of mildly affected children.

Long-term somatic follow-up of prenatally treated children with congenital adrenal hyperplasia.

Prenatal virilization of female fetuses is a serious symptom associated with severe congenital adrenal hyperplasia. In attempt to avoid sexual ambiguity, prenatal treatment of 21-hydroxylase deficiency was initiated in 1984, with the first Scandinavian case treated in 1985. Here we have studied the outcome of prenatal diagnosis and therapy of 44 at-risk pregnancies monitored during the years 1985-1995 in Scandinavia. Treated mothers and children were compared with matched controls. Compared to their elder affected sisters, all 5 girls with severe congenital adrenal hyperplasia who were treated until term showed little virilization. Only 1 required surgery for labial fusion. The majority of the 44 dexamethasone-treated fetuses demonstrated normal pre- and postnatal growth compared to matched controls. However, several adverse events such as failure to thrive and delayed psychomotor development, were reported among the treated infants. In addition, treated mothers reported more side-effects during pregnancy than did controls. A significant increase in weight gain was observed during early pregnancy when treatment was initiated, but this initial rapid weight gain declined during late pregnancy or when treatment was terminated. Thus, experience to date suggests that prenatal treatment of affected female fetuses is generally efficient in minimizing virilization of external genitalia. However, there is still a need to collect more data concerning possible rare unfavorable effects of this therapy on mother and child.

Functional analysis of two recurrent amino acid substitutions in the CYP21 gene from Italian patients with congenital adrenal hyperplasia.

Congenital adrenal hyperplasia (CAH) is most commonly due to 21-hydroxylase deficiency and presents a wide spectrum of clinical manifestations from a severe classical form to a milder late-onset form with a variable severity of hyperandrogenic symptoms. A limited number of mutations account for the majority of the mutated alleles, but additional rare mutations are responsible for the symptoms in some patients. By CYP21 gene analysis, we identified a chimeric CYP21P/CYP21 gene with the fusion breakpoint downstream of the common P30L mutation as well as a GCC to ACC change at codon 15 (A15T) in two subjects with classical CAH and a CCC to TCC change at codon 482 (P482S) in seven subjects referred for nonclassical CAH, precocious pubarche, menstrual irregularities, or hypertrichosis. The two amino acid substitutions were reconstructed by in vitro site-directed mutagenesis, the proteins were transiently expressed in COS-1 cells, and enzyme activity toward the two natural substrates (17-hydroxyprogesterone and progesterone) was determined. The A15T mutant exhibited no significant difference in activity compared with the wild-type protein, whereas the P482S mutation reduced enzyme activity to 70% of normal. This impairment of activity was confirmed in vivo by detection of heterozygote carriers by the ACTH test.

Prophylactic adrenalectomy of a three-year-old girl with congenital adrenal hyperplasia: pre- and postoperative studies.

Long term follow-up studies of children with congenital adrenal hyperplasia have documented less than desirable outcomes, including reduction in final adult height, obesity, virilism, and decreased fertility. We have proposed that children with the most severe forms of congenital adrenal hyperplasia would be better off if their adrenals were removed at an early age. We report here on our experience with prophylactic bilateral adrenalectomy in a 3-yr-old girl with a double null mutation of the CYP21 gene. The results of sodium balance studies, performed preoperatively on our patient and her unaffected fraternal twin sister, and hormonal data are presented as well. In contrast to her twin, who markedly increased her sodium retention in response to ACTH, our patient showed increased natriuresis, suggesting a deleterious effect of her adrenals on sodium homeostasis. Adrenalectomy was carried out at the time of necessary genital repair. No surgical or postsurgical complications were encountered.

Preserved male fertility despite decreased androgen sensitivity caused by a mutation in the ligand-binding domain of the androgen receptor gene.

Mutations in the androgen receptor gene are considered as incompatible with preservation of fertility and have been suggested as a cause of male infertility. Two adult brothers, referred because of gynecomastia and hormonal levels in serum indicating androgen insensitivity (high sex hormone-binding globulin, and LH levels, despite extremely high testosterone concentration), turned out to be relatives to a third young man, referred independently of the two others and exhibiting identical clinical and hormonal stigmata. In all three men, we found a C-->A substitution at position 2470 (exon 7) in the androgen receptor gene, leading to a Gln824Lys mutation in the ligand-binding domain of the receptor. Exploring the family history revealed that their grandfathers, on their mothers' side, were brothers; and the Gln824Lys mutation was also found in the one of them who was still alive. Binding studies with the mutant receptor in transfected COS-7 cells, with mibolerone as ligand, exhibited equal Kd (0.7 vs. 1.0 nmol/ L), IC50 (0.8 vs. 1.1 nmol/L), and maximum binding (7.1 vs. 8.9 fmol/ 10(6) cells), as compared with the wild-type (WT) receptor. In a chloramphenicol acetyl transferase trans-activation assay, the activity of the mutant receptor was identical to that of the WT, when the synthetic androgen R1881 was'used as a ligand; but with dihydrotestosterone, in concentrations up to 10 nmol/L, the activity of Gln824Lys mutated receptor was 10-62% of the WT variant. Thus, Gln824Lys mutation was found, both in vivo and in vitro, to cause slight impairment of receptor function but was compatible with preservation of male fertility. The patients inherited the mutation from their grandfathers through their mothers, and one of the young men possessing the mutation has fathered a daughter.

Molecular approaches for the diagnosis of 21-hydroxylase deficiency and congenital adrenal hyperplasia.

Congenital adrenal hyperplasia due to 21-hydroxylase deficiency results in deficiency of cortisol and aldosterone and overproduction of androgens. The 21-hydroxylase locus has a complicated structure, with a highly homologous pseudogene (CYP21P) and an active gene (CYP21) in tandem repeats, a high degree of interindividual variation in gene copy numbers, and exchange of sequences between CYP21P and CYP21. Nine mutations, representing sequences that are normally present in the pseudogene, account for about 95% of all affected CYP21 alleles. Accurate and rapid diagnostic evaluation of congenital adrenal hyperplasia due to 21-hydroxylase deficiency can be performed by typing directly for disease-causing mutations using allele-specific polymerase chain reaction (PCR). A strong correlation exists between genotype and phenotype; mutational analysis can be used to predict disease severity in affected individuals.

An update on the molecular genetics of congenital adrenal hyperplasia: diagnostic and therapeutic aspects.

An update on the molecular genetics of congenital adrenal hyperplasia due to 21-hydroxylase deficiency is given. In Sweden, direct mutation detection has been used for genetic diagnosis of this disease since 1990. Around 400 affected 21-hydroxylase genes have been analyzed so far. Mutations that have arisen by interaction with the adjacent pseudogene, including gene deletion and nine smaller sequence aberrations, are responsible for the disease in around 95% of alleles. A total of 13 rare, mostly population-specific mutations have been characterized among the remaining 5%. Some of these rare mutations are present in the pseudogene at a low frequency, indicating that they have started to spread at a low rate in the population. The mutations can be divided into different groups according to severity. This makes it possible to predict clinical outcome in affected subjects based on genotyping. The risk of salt-wasting and prenatal virilization can be estimated, and overtreatment can be avoided in mildly affected cases.

ABC relaxation theory and the factor structure of relaxation states, recalled relaxation activities, dispositions, and motivations.

ABC Relaxation Theory proposes 15 psychological relaxation-related states (R-States): Sleepiness, Disengagement, Physical Relaxation, Mental Quiet, Rested/Refreshed, At Ease/At Peace, Energized, Aware, Joy, Thankfulness and Love, Prayerfulness, Childlike Innocence, Awe and Wonder, Mystery, and Timeless/Boundless/Infinite. The present study summarizes the results of 13 separate factor analyses of immediate relaxation-related states, states associated with recalled relaxation activities, relaxation dispositions, and relaxation motivations on a combined sample of 1,904 individuals (group average ages ranged from 28-40 yr.). Four exploratory factor analyses of Smith Relaxation Inventories yielded 15 items that most consistently and exclusively load (generally at least .70) on six replicated factors. These items included happy, joyful, energized, rested, at peace, warm, limp, silent, quiet, dozing, drowsy, prayerful, mystery, distant, and indifferent. Subsequent factor analyses restricted to these items and specifying six factors were performed on 13 different data sets. Each yielded the same six-factor solution: Factor 1: Centered Positive Affect, Factor 2: Sleepiness, Factor 3: Disengagement, Factor 4: Physical Relaxation, Factor 5: Mental Quiet, and Factor 6: Spiritual. Implications for ABC Relaxation Theory are discussed.

[Boy or girl? Molecular mechanisms in sex differentiation]. / Pojke eller flicka? Molekylära mekanismer vid könsdifferentiering.

A growing number of factors have been recognized as crucial in sexual development, and many clinical conditions have become understandable as mutations in relevant genes have been identified. In some cases this has led to the development of DNA diagnostics, which can be of some aid in the workup of this type of patient. So far it is mainly more serious disorders which have been elucidated, thanks to the identification of extensive mutations in the key genes for sexual development. Exactly to what extent less severe damage in these genes underlies more subtle disorders of sexual development, such as disturbances in pubertal development and diminished fertility, is with few exceptions unknown. We are still aware of only a fraction of the information hidden in our genetic heritage. Developments in this field are nonetheless rapid, and molecular analyses will probably become more and more part and parcel of the workup of patients with a wide variety of disturbances in sexual development.