Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging.

Genome sequencing has established clinical utility for rare disease diagnosis. While increasing numbers of individuals have undergone elective genome sequencing, a comprehensive study surveying genome-wide disease-associated genes in adults with deep phenotyping has not been reported. Here we report the results of a 3-y precision medicine study with a goal to integrate whole-genome sequencing with deep phenotyping. A cohort of 1,190 adult participants (402 female [33.8%]; mean age, 54 y [range 20 to 89+]; 70.6% European) had whole-genome sequencing, and were deeply phenotyped using metabolomics, advanced imaging, and clinical laboratory tests in addition to family/medical history. Of 1,190 adults, 206 (17.3%) had at least 1 genetic variant with pathogenic (P) or likely pathogenic (LP) assessment that suggests a predisposition of genetic risk. A multidisciplinary clinical team reviewed all reportable findings for the assessment of genotype and phenotype associations, and 137 (11.5%) had genotype and phenotype associations. A high percentage of genotype and phenotype associations (>75%) was observed for dyslipidemia (n = 24), cardiomyopathy, arrhythmia, and other cardiac diseases (n = 42), and diabetes and endocrine diseases (n = 17). A lack of genotype and phenotype associations, a potential burden for patient care, was observed in 69 (5.8%) individuals with P/LP variants. Genomics and metabolomics associations identified 61 (5.1%) heterozygotes with phenotype manifestations affecting serum metabolite levels in amino acid, lipid and cofactor, and vitamin pathways. Our descriptive analysis provides results on the integration of whole-genome sequencing and deep phenotyping for clinical assessments in adults.

Changes in plasma and urine globotriaosylceramide levels do not predict Fabry disease progression over 1 year of agalsidase alfa.

PURPOSE: Globotriaosylceramide concentrations were assessed as potential predictors of change from baseline after 12 months by estimated glomerular filtration rate and left-ventricular mass index using pooled data from three randomized, placebo-controlled agalsidase alfa trials and open-label extensions of patients with Fabry disease. METHODS: Males (aged 18 years or older) with Fabry disease received agalsidase alfa (0.2 mg/kg every other week for 12 months). A backward-elimination approach evaluated potential predictors (baseline estimated glomerular filtration rate and left-ventricular mass index; age at first dose; baseline and change from baseline at 12 months of globotriaosylceramide (urine, plasma); urine protein excretion; and systolic and diastolic blood pressure). Subgroups included patients randomized to placebo or agalsidase alfa (double-blind phase), then to agalsidase alfa (open-label extensions; placebo→agalsidase alfa or agalsidase alfa→agalsidase alfa, respectively) and stage 2/3 chronic kidney disease patients. RESULTS: Baseline estimated glomerular filtration rate, age at first dose, baseline urine globotriaosylceramide excretion, and baseline and change from baseline urine protein excretion significantly predicted change from baseline estimated glomerular filtration rate in the analysis population (N = 73; all P<0.05), although not in all subgroups. Change from baseline urine and plasma globotriaosylceramide (baseline and change from baseline) concentrations did not predict change from baseline estimated glomerular filtration rate. No predictors of left-ventricular mass index were significant. CONCLUSION: Changes in globotriaosylceramide concentrations do not appear to be useful biomarkers for prediction of Fabry disease-related changes in estimated glomerular filtration rate or left-ventricular mass index.

Postpartum thrombotic microangiopathic syndrome.

OBJECTIVE: Characterization of syndromes for patients with life-threatening, progressively worsening hemolysis-elevated-liver-enzymes-and-platelet (HELLP) syndrome-like diseases and with thrombotic microangiopathies. RETROSPECTIVE STUDY DESIGN: Patients who underwent postpartum plasma-exchange (PPEX) for preeclampsia-related, and microangiopathy/coagulopathy illnesses unresponsive to medical therapy between 1994 and 2008 in our center and elsewhere. RESULTS: Nine patients were treated with PPEX in our center with 78% maternal survival. Treatment with PPEX increased platelet levels (p=0.048), decreased serum lactic dehydrogenase (p=0.0012) and aspartate aminotransferase (p=0.0001). CONCLUSION: Nineteen patients from publications combined with our patients suggest five categories of postpartum thrombotic microangiopathy syndrome that exhibit HELLP syndrome criteria and respond to PPEX.

Prevention of ulceration, amputation, and reduction of hospitalization: outcomes of a prospective multicenter trial of tibial neurolysis in patients with diabetic neuropathy.

This is the first multicenter prospective study of outcomes of tibial neurolysis in diabetics with neuropathy and chronic compression of the tibial nerve in the tarsal tunnels. A total of 38 surgeons enrolled 628 patients using the same technique for diagnosis of compression, neurolysis of four medial ankle tunnels, and objective outcomes: ulceration, amputation, and hospitalization for foot infection. Contralateral limb tibial neurolysis occurred in 211 patients for a total of 839 operated limbs. Kaplan-Meier proportional hazards were used for analysis. New ulcerations occurred in 2 (0.2%) of 782 patients with no previous ulceration history, recurrent ulcerations in 2 (3.8%) of 57 patients with a previous ulcer history, and amputations in 1 (0.2%) of 839 at risk limbs. Admission to the hospital for foot infections was 0.6%. In patients with diabetic neuropathy and chronic tibial nerve compression, neurolysis can result in prevention of ulceration and amputation, and decrease in hospitalization for foot infection.

A positive Tinel sign as predictor of pain relief or sensory recovery after decompression of chronic tibial nerve compression in patients with diabetic neuropathy.

Predictive ability of a positive Tinel sign over the tibial nerve in the tarsal was evaluated as a prognostic sign in determining sensory outcomes after distal tibial neurolysis in diabetics with chronic nerve compression at this location. Outcomes were evaluated with a visual analog score (VAS) for pain and measurements of the cutaneous pressure threshold/two-point discrimination. A multicenter prospective study enrolled 628 patients who had a positive Tinel sign. Of these patients, 465 (74%) had VAS >5. Each patient had a release of the tarsal tunnel and a neurolysis of the medial and lateral plantar and calcaneal tunnels. Subsequent, contralateral, identical surgery was done in 211 of the patients (152 of which had a VAS >5). Mean VAS score decreased from 8.5 to 2.0 (p <0.001) at 6 months, and remained at this level for 3.5 years. Sensibility improved from a loss of protective sensation to recovery of some two-point discrimination during this same time period. It is concluded that a positive Tinel sign over the tibial nerve at the tarsal tunnel in a diabetic patient with chronic nerve compression at this location predicts significant relief of pain and improvement in plantar sensibility.

Long-term, open-labeled extension study of idursulfase in the treatment of Hunter syndrome.

PURPOSE: This study evaluated the safety and effectiveness of long-term enzyme replacement therapy with idursulfase (recombinant human iduronate-2-sulfatase) in patients with Hunter syndrome. METHODS: All 94 patients who completed a 53-week double-blinded study of idursulfase enrolled in this open-labeled extension study and received intravenous idursulfase at a dose of 0.5 mg/kg weekly for 2 years, and clinical outcomes and safety were assessed. RESULTS: No change in percent predicted forced vital capacity was seen, but absolute forced vital capacity demonstrated sustained improvement and was increased 25.1% at the end of the study. Statistically significant increases in 6-minute walking test distance were observed at most time points. Mean liver and spleen volumes remained reduced throughout the 2-year extension study. Mean joint range of motion improved for the shoulder and remained stable in other joints. Both the parent- and child-assessed Child Health Assessment Questionnaire Disability Index Score demonstrated significant improvement. Infusion-related adverse events occurred in 53% of patients and peaked at Month 3 of treatment and declined thereafter. Neutralizing IgG antibodies were detected in 23% of patients and seemed to attenuate the improvement in pulmonary function. CONCLUSIONS: Weekly infusions of idursulfase result in sustained clinical improvement during 3 years of treatment.

Women with preterm premature rupture of the membranes do not benefit from weekly progesterone.

OBJECTIVE: We sought to determine if 17-alpha-hydroxyprogesterone (17P) extends gestation vs placebo in women with preterm premature rupture of the membranes (PPROM). STUDY DESIGN: Women with vertex presentations with PPROM, 20-30 weeks' gestation, were randomized to receive weekly 17P or placebo in an attempt to prolong the pregnancy. A total of 69 patients (17P, n = 33; placebo, n = 36) were randomized into this study. RESULTS: Initial cervical dilatation, gestational age at enrollment, and interval to delivery were not different between the 2 groups (P = .914, .424, and .146, respectively). Time of randomization to delivery (P = .250), mode of delivery (relative risk, 1.16; 95% confidence interval, 0.66-2.06), and the neonatal outcome statistics of morbidity (P = .820) and mortality (relative risk, 1.28; 95% confidence interval, 0.59-2.75) were similar between the 2 groups. CONCLUSION: In patients with PPROM, 17P did not extend gestation vs placebo and cannot be recommended for treatment in such women.

Four-year prospective clinical trial of agalsidase alfa in children with Fabry disease.

OBJECTIVES: To investigate a 4-year prospective clinical trial of agalsidase alfa in children with Fabry disease, an X-linked metabolic disorder caused by a deficiency of the lysosomal enzyme alpha-galactosidase A. STUDY DESIGN: Seventeen (16 boys, 1 girl; age range, 7.3 to 18.4 years) of the 24 children who completed a 6-month, open-label agalsidase alfa study enrolled in a 3.5-year extension study that investigated the safety and potential efficacy of long-term treatment. All 17 patients completed the initial 6-month study, and 10 patients (9 boys) completed the extension study. RESULTS: Agalsidase alfa was well tolerated. In treated boys, there were sustained, statistically-significant improvements in the clinical features of Fabry disease, including reduced plasma globotriaosylceramide levels, reduced pain severity assessed by the Brief Pain Index, and improved heart rate variability. Mean urine globotriaosylceramide levels were reduced to normal range (P < .05 compared with baseline during 1.5 to 4 years). Kidney function and left ventricular mass indexed to height remained stable throughout. CONCLUSIONS: This clinical trial demonstrates that treatment with agalsidase alfa was well tolerated and associated with improvement of Fabry disease-related features.

Diagnostic criteria and tumor screening for individuals with isolated hemihyperplasia.

Isolated hemihyperplasia, formerly termed isolated hemihypertrophy, is a congenital overgrowth disorder associated with an increased risk for embryonal tumors, mainly Wilms tumor and hepatoblastoma. This practice guideline will set forth the diagnostic criteria and tumor screening recommendations for children with isolated hemihyperplasia, based on the best information available. There is clinical overlap between isolated hemihyperplasia with Beckwith-Wiedemann syndrome. The majority of Beckwith-Wiedemann syndrome patients have a molecular abnormality involving the imprinted cluster of genes at 11p15.5. In contrast, the preponderance of isolated hemihyperplasia patients studied have no identified etiology. Tumors have developed in isolated hemihyperplasia patients with and without molecular abnormalities. For this reason, molecular diagnostics are not helpful in identifying the subset of isolated hemihyperplasia patients with tumor risk and all isolated hemihyperplasia patients should undergo tumor screening.

Whorl patterns on the lower lip are associated with nonsyndromic cleft lip with or without cleft palate.

Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common birth defect due to both genetic and environmental factors. Whorl lip print patterns are circular grooves on the central upper lip and/or the left and right lower lip. To determine if whorls are more common in families with CL/P than in controls, the Pittsburgh Orofacial Cleft Study collected lip prints from over 450 subjects, that is, individuals with CL/P, their relatives, and unrelated controls-from the U.S., Argentina, and Hungary. Using a narrow definition of lower-lip whorl, the frequency of whorls in the U.S. sample was significantly elevated in cleft individuals and their family members, compared to unrelated controls (14.8% and 13.2% vs. 2.3%; P = 0.003 and 0.001, respectively). Whorls were more frequent in CL/P families from Argentina than in CL/P families from the U.S. or Hungary. If these results are confirmed, whorl lip print patterns could be part of an expanded phenotypic spectrum of nonsyndromic CL/P. As such, they may eventually be useful in a clinical setting, allowing recurrence risk calculations to incorporate individual phenotypic information in addition to family history data.

Progesterone does not prevent preterm births in women with twins.

OBJECTIVE: To compare preterm birth rate and neonatal outcome in twin gestations randomized to either 17 alpha-hydroxyprogesterone caproate (17P) or placebo. MATERIALS AND METHODS: Women with twin gestations between 20-30 weeks were randomized to receive weekly injections of either 250 mg 17P injection (Group I), or placebo (Group II). Maternal and neonatal outcome data was recorded. RESULTS: Thirty twin intrauterine pregnancies were randomized; 16 received 17P and 14 received placebo. Demographic data as well as past history and gestational age at randomization were equivalent between groups (P = 0.286-0.847). All patients in both groups were Medicaid recipients. The incidence of preterm labor (P = 0.980), and premature rupture of the membranes (P = 0.525) were the same between groups. Gestational age at delivery was also similar between 17P (33.9 weeks) versus placebo (33.1 weeks, P = 0.190) as was the incidence of preterm birth <35 weeks (44% vs 79%, P = 0.117). Infant weight (P = 0.641), Apgar score at 5 minutes (P = 0.338) as well as neonatal morbidity such as respiratory distress syndrome (P = 0.838), patent ductus arteriosus (P = 0.704), intraventricular hemorrhage (P = 0.851) and necrotizing enterocolitis (P = 0.946) showed no difference. Days spent in the NICU among 17P (18.4) versus placebo (17.3, P = 0.155), neonatal death (P = 0.359) and those infants discharged with neurologic handicap (P = 0.594) were not different between groups. CONCLUSION: Amongst this group of twin gestations weekly 17HP injections did not reduce the incidence of preterm birth or the complications associated with prematurity.

AXIS inhibition protein 2, orofacial clefts and a family history of cancer.

BACKGROUND: Cancer and congenital malformations occasionally may have a common etiology. The authors investigated whether families with one or more members affected by orofacial clefts (that is, families segregating orofacial clefts) had an increased cancer incidence when compared with control families. METHODS: The authors assessed 75 white families with nonsyndromic cleft lip with or without cleft palate (CL/P) and 93 white control families regarding a history of cancer. They used chi(2) and Fisher exact tests to determine significant differences. They then performed molecular studies with genes in which mutations have been independently associated with both cancer and craniofacial anomalies in a total of 111 families with CL/P. RESULTS: The families with CL/P reported a family history of cancer more often than did control families (P <.001), and they had higher rates of specific cancer types: colon (P <.001), brain (P = .003), leukemia (P = .005), breast (P = .009), prostate (P = .01), skin (P = .01), lung (P = .02) and liver (P = .02). The authors detected overtransmission of AXIS inhibition protein 2 (AXIN2) in CL/P probands (P = .003). CONCLUSION: Families segregating CL/P may have an increased susceptibility to cancer, notably colon cancer. Furthermore, AXIN2, a gene that when mutated increases susceptibility to colon cancer, also is associated with CL/P. CLINICAL IMPLICATIONS: People who are at a higher risk of developing disease need to adopt a healthier lifestyle, including avoiding exposure to risk factors that may interact with their genotypes.

Initial report from the Hunter Outcome Survey.

PURPOSE: Hunter syndrome (Mucopolysaccharidosis II) is a rare, X-linked disorder of glycosaminoglycan metabolism. It is caused by a deficiency in the lysosomal enzyme iduronate-2-sulfatase, and in affected patients glycosaminoglycan accumulates in lysosomes of various tissues and organs and contributes to the pathophysiology of Hunter syndrome. The Hunter Outcome Survey (HOS) was established to better describe the natural history of this disorder and to evaluate the long-term effect of enzyme replacement therapy. METHODS: HOS is an international, multicenter, long-term observational survey that will collect data on participating patients with a confirmed diagnosis of Hunter syndrome. Data will be collected during regular physician examinations and entered into an electronic database. Examples of observations include vital signs, laboratory values, signs and symptoms of organ involvement, and the results of selected functional tests (e.g., audiometry, echocardiogram, joint mobility, etc.). RESULTS: As of May 15, 2007, 263 patients from 16 countries have enrolled in HOS; 24% of these patients were currently being treated with enzyme replacement therapy. The median age at enrollment was 12.2 years. The median age of onset of symptoms and diagnosis of Hunter syndrome were 1.5 and 3.5 years, respectively. Otitis media and abdominal hernia were the earliest presenting symptoms. Facial dysmorphism and hepatosplenomegaly were demonstrated by 95% and 89% of patients, respectively. CONCLUSIONS: HOS will be a valuable resource for enhancing the understanding of Hunter syndrome and will provide important information about the natural history of the disease and the role of enzyme replacement therapy in its treatment. Patients and their physicians should be encouraged to participate.

Development and validation of a measure of dysmorphology: useful for autism subgroup classification.

Autism spectrum disorders (ASD) comprise a class of neurodevelopmental disorders that can originate from a variety of genetic and environmental causes. To delineate autism's heterogeneity we have looked for biologically-based phenotypes found in consistent proportions of ASD individuals. One informative phenotype is that of generalized dysmorphology, based on whole body examinations by medical geneticists trained in the nuances of anomalous embryologic development. We identified a need for a dysmorphology measure that could be completed by medical clinicians not extensively trained in dysmorphology that would still retain the level of sensitivity and specificity of the comprehensive dysmorphology examination. Based on expert-derived consensus dysmorphology designation of 222 autism patients and a classification validation study of 30 subjects by four dysmorphologists, we determined that dysmorphology designations based on body areas provided superior inter-rater reliability. Using 34 body area designations, we performed a classification and regression tree (CART) analysis to construct a scoring algorithm. Compared to the consensus classification, the model performed with 81% sensitivity and 99% specificity, and classification of a replication dataset of 31 ASD individuals performed well, with 82% sensitivity and 95% specificity. The autism dysmorphology measure (ADM) directs the clinician to score 12 body areas sequentially to arrive at a determination of "dysmorphic" or "nondysmorphic." We anticipate the ADM will permit clinicians to differentiate accurately between dysmorphic and nondysmorphic individuals-allowing better diagnostic classification, prognostication, recurrence risk assessment, and laboratory analysis decisions-and research scientists to better define more homogeneous autism subtypes.

Pregnancy loss after first trimester viability in women with sickle cell trait: a preliminary report.

BACKGROUND: Traditionally, sickle cell trait has not been associated with a higher risk of fetal death, but we noted several, which led us to assess all such pregnancies. METHODS: In this retrospective study, 131 patients with sickle cell trait were analyzed over a two-year period. The Institutional Review Board approved the collection of deidentified data. RESULTS: Subjects were African-American with an average age of 23.9 years, and average gestational age at delivery of 30.1 weeks. There were 10 (8.13%) intrauterine fetal deaths (IUFDs), and one neonatal death. Ascending amniotic fluid infection was noted in 50% and 92% meconium histocytes. All placentas had sickling in the intervillous space and the decidual vessels. CONCLUSIONS: Sickling in the decidual vessels and poor placental perfusion may play a role in pregnancy loss in excess of what has previously been reported. A cohort control study appears to be in order. NARRATIVE: Pregnant women with sickle cell trait are thought not to have increased maternal or fetal mortality/morbidity. Over a two year period, we studied 131 women with this hemoglobinopathy and found that 10.6% had intrauterine growth retardation (IUGR), 8.4% preterm premature rupture of the membranes, 8.1% intrauterine fetal demise (n = 10) at most occurring at 16 to 24 weeks, and one neonatal death. Amniotic fluid infection was noted in 50%, and meconium histocytes indicating intrauterine hypoxia were noted, as was unsuspected sickling in the placental vasculature. Based on this case series, sickle cell trait may not be as benign for the fetus as was previously thought.

Metformin and insulin in the management of gestational diabetes mellitus: preliminary results of a comparison.

OBJECTIVE: To compare glycemic control and neonatal outcomes in women with gestational diabetes mellitus (GDM) treated with metformin vs. insulin. STUDY DESIGN: Women with GDM not controlled with diet and exercise were randomized to metformin (n = 32) or insulin (n = 31). The levels of glycemic control as well as maternal/neonatal complications were evaluated. RESULTS: The mean (+/- SD) fasting and 2-hour postprandial blood glucose did not differ statistically between the 2 treatment groups. No patient failed metformin and required insulin. The majority (27/32) were easily controlled on the initial dosage (500 mg twice a day). Gestational age at entry and delivery (p = 0.077, 0.412) were similar. The difference in the rate of cesarean delivery was not statistically significant between the 2 groups (p = 0.102). Neonatal statistics were also not different between the metformin and insulin groups: birth weight, Apgar score at 5 minutes, respiratory distress syndrome, hyperbilirubinemia, neonatal hypoglycemia and neonatal intensive care unit admission (p = 0.144-0.373). CONCLUSION: Based on these preliminary data, metformin appears to be an effective alternative to insulin in the treatment of GDM.

Tocolytic preference for treatment of preterm labor.

Preterm labor remains the most common complication of pregnancy. Although tocolytic treatment is the standard of care in such women, there is no FDA approved drug for therapy, and there is no unanimity of drug regimens among physicians. This survey details the patterns of twenty Maternal-Fetal Medicine specialists who manage over 6,000 cases of preterm labor with intact membranes annually. Approximately 90% of women were seen early enough to be effectively treated with tocolytics, and over 90% of these subjects received corticosteroids. First-line tocolytic use favored magnesium sulfate while antiprostaglandin drugs were the leading second-line drug whereas intravenous terbutaline and calcium channel antagonists were used less often. There were many different dosage patterns for each drug as well as combinations of various tocolytic drugs which were individually adjusted for patient circumstances. Women with preterm labor and intact membranes are usually treated with tocolytics and corticosteroids, but regimens are varied and all use is off label. This study demonstrates the need for an FDA approved tocolytic which could be used consistently for such women.

Pregnancy loss after first-trimester viability in women with sickle cell trait: time for a reappraisal?

OBJECTIVE: The purpose of this study was to evaluate the obstetric outcomes and pathologic findings in women with sickle cell trait. STUDY DESIGN: In this retrospective case control study, pregnant women with sickle cell trait were studied over a 4-year period (2001-2005). The women who were delivered at > 16 weeks of gestation were compared with a cohort group of subjects with normal hemoglobin levels, and the placentas were sent for pathologic evaluation. RESULTS: A total of 180 pregnancies were studied with a like number of control patients. Subjects who had sickle cell trait demonstrated shorter average duration of pregnancy (233 +/- 45 days vs 255 +/- 34 days; P < .001) and lower birth weight (2114 +/- 1093 g vs 2672 +/- 942 g; P < .001). The rate of fetal death was significantly higher among study group patients (3.5% vs 9.7%; P = .015) when compared with the control group. Additionally, in study women, acute ascending amniotic infection and meconium histiocytosis were noted much more frequently. Sickling in the intervillous space and decidual vessels that were not associated with artifactual change was also found among patients sickle cell trait. CONCLUSION: Patients with sickle cell trait appear to be at increased risk for fetal loss compared with women with normal hemoglobin levels, and placental abnormalities may play a causal role.

Tocolysis in women with advanced preterm labor: a secondary analysis of a randomized clinical trial.

OBJECTIVE: To compare the efficacy of tocolytic treatment with indomethacin (I), magnesium sulfate (M) and nifedipine (N) for acute tocolysis in women with advanced cervical dilation (4-6 cm). METHODS: A single center, randomized trial was carried out involving patients in preterm labor (cervix 1-6 cm). Secondary analysis of women with advanced cervical dilation (cervix 4-6 cm) at 24-32 weeks' gestation who received intravenous M, oral N or I suppositories comprised this study population. RESULTS: Over 38 months, 92 women with advanced cervical dilation were randomized to one tocoloytic type. Days gained in utero (11.7) and percent remaining undelivered at 48 h (60.8%), 72 h (53.1%) and >7 days (38.3%) were similar regardless of tocolytic employed (p = 0.923, 0.968, 0.791, 0.802, respectively). Likewise, gestational age at delivery (30.7 ± 3.2) was similar between groups (p = 0.771). Finally, neonatal statistics were not different when stratified by tocolytic treatment. CONCLUSION: There were no statistical differences between tocolytics in treating women with advanced cervical dilation. All offered significant days gained in utero after therapy, a high percentage remaining undelivered after 48 or 72 h and after 7 days. It would appear from data that there may be advantages to tocolytic treatment even in women with advanced cervical dilation.