Pediatric medicine and the genetic disorders of the Amish and Mennonite people of Pennsylvania

Newborn screening for severe combined immunodeficiency and inborn errors of immunity

PURPOSE OF REVIEW

Severe combined immune deficiency (SCID) is the most devastating genetic disease of the immune system with an unfavorable outcome unless diagnosed early in life. Newborn screening (NBS) programs play a crucial role in facilitating early diagnoses and timely interventions for affected infants.

RECENT FINDINGS

SCID marked the pioneering inborn error of immunity (IEI) to undergo NBS, a milestone achieved 15 years ago through the enumeration of T-cell receptor excision circles (TRECs) extracted from Guthrie cards. This breakthrough has revolutionized our approach to SCID, enabling not only presymptomatic identification and prompt treatments (including hematopoietic stem cell transplantation), but also enhancing our comprehension of the global epidemiology of SCID.

SUMMARY

NBS is continuing to evolve with the advent of novel diagnostic technologies and treatments. Following the successful implementation of SCID-NBS programs, a call for the early identification of additional IEIs is the next step, encompassing a broader spectrum of IEIs, facilitating early diagnoses, and preventing morbidity and mortality.

Updated Management Guidelines for Adenosine Deaminase Deficiency

Inherited defects in the adenosine deaminase (ADA) gene typically cause severe combined immunodeficiency. In addition to infections, ADA-deficient patients can present with neurodevelopmental, behavioral, hearing, skeletal, lung, heart, skin, kidney, urogenital, and liver abnormalities. Some patients also suffer from autoimmunity and malignancies. In recent years, there have been remarkable advances in the management of ADA deficiency. Most ADA-deficient patients can be identified by newborn screening for severe combined immunodeficiency, which facilitates early diagnosis and treatment of asymptomatic infants. Most patients benefit from enzyme replacement therapy (ERT). Allogeneic hematopoietic cell transplantation from an HLA-matched sibling donor or HLA-matched family member donor with no conditioning is currently the preferable treatment. When matched sibling donor or matched family member donor is not available, autologous ADA gene therapy with nonmyeloablative conditioning and ERT withdrawal, which is reported in recent studies to result in 100% overall survival and 90% to 95% engraftment, should be pursued. If gene therapy is not immediately available, ERT can be continued for a few years, although its excessive cost might be prohibitive. The recent improved outcome of hematopoietic cell transplantation using HLA-mismatched family-related donors or HLA-matched unrelated donors, after reduced-intensity conditioning, suggests that such procedures might also be considered rather than continuing ERT for prolonged periods. Long-term follow-up will further assist in determining the optimal treatment approach for ADA-deficient patients.

Postoperative Outcomes in the Plain Community Population of Western Wisconsin

BACKGROUND

Residents of plain communities constitute an underserved minority population that is not reliably captured in contemporary surgical outcomes research. We hypothesized that plain communities (PC) patients would have higher postoperative complication rates than a general surgical population.

METHODS

A retrospective review of 30-day postoperative outcomes for PC patients compared to a majority (non-PC) matched patient population from September 2014 to March 2020 was performed. The primary outcome measure was any complication within 30 days of surgery.

RESULTS

270 PC patients were matched with 493 non-PC patients. The 30-day complication rate was higher for the PC group (6.3% vs 3.7%, P = .09), though not statistically significant. There was significantly lower utilization of preventive care services, and postoperative follow-up among PC patients.

DISCUSSION

Although our regional PC surgical patient population utilized preventive and postoperative health care services less than the non-PC population, there was no statistically significant difference in overall 30-day postoperative morbidity or mortality.

The burden of pathogenic variants in clinically actionable genes in a founder population

Founder populations may be enriched with certain genetic variants of high clinical impact compared to nonfounder populations due to bottleneck events and genetic drift. Using exome sequencing (ES), we quantified the load of pathogenic variants that may be clinically actionable in 6136 apparently healthy adults living in the Lancaster, PA Old Order Amish settlement. We focused on variants in 78 genes deemed clinically actionable by the American College of Medical Genetics and Genomics (ACMG) or Geisinger's MyCode Health Initiative. ES revealed 3191 total variants among these genes including 480 nonsynonymous variants. After quality control and filtering, we applied the ACMG/AMP guidelines for variant interpretation and classified seven variants, across seven genes, as either pathogenic or likely pathogenic. Through genetic drift, all seven variants, are highly enriched in the Amish compared to nonfounder populations. In total, 14.7% of Lancaster Amish individuals carry at least one of these variants, largely explained by the 13% who harbor a copy of a single variant in APOB. Other studies report combined frequencies of pathogenic/likely pathogenic (P/LP) variants in actionable genes between 2.0% and 6.2% in outbred populations. The Amish population harbors fewer actionable variants compared to similarly characterized nonfounder populations but have a higher frequency of each variant identified, offering opportunities for efficient and cost-effective targeted precision medicine.

Under-referral of Plain community members for genetic services despite being qualified for genetic evaluation

Plain community people (Amish and Mennonites) have increased risk of having recessive genetic disorders. This study was designed to assess the rate of referral of Plain people to genetic services at UPMC Children’s Hospital of Pittsburgh. Medical records of Plain patients from a 1-year time period were reviewed. Data collected included demographic information, clinical presentation, referral for genetic services, and diagnosis. Of the 303 patients, 102 (33.7%) had a clinical presentation suggestive of a genetic disorder, yet only 32 of those 102 patients (31.4%) had been evaluated by the division of Medical Genetics. These data indicate that less than half of Plain patients with a clinical presentation suggestive of a genetic disorder had been referred to the division of Medical Genetics for a formal evaluation. Now that under-referral of Plain patients has been confirmed, providers can be educated in order to increase referrals for genetic services and facilitate positive healthcare outcomes for the Plain Community.

Gene Therapy for Primary Immunodeficiency

Over the past 3 decades, there has been significant progress in refining gene therapy technologies and procedures. Transduction of hematopoietic stem cells ex vivo using lentiviral vectors can now create a highly effective therapeutic product, capable of reconstituting many different immune system dysfunctions when reinfused into patients. Here, we review the key developments in the gene therapy landscape for primary immune deficiency, from an experimental therapy where clinical efficacy was marred by adverse events, to a commercialized product with enhanced safety and efficacy. We also discuss progress being made in preclinical studies for challenging disease targets and emerging gene editing technologies that are showing promising results, particularly for conditions where gene regulation is important for efficacy.

Glutaric acidemia type 1: Treatment and outcome of 168 patients over three decades

Glutaric acidemia type 1 (GA1) is a disorder of cerebral organic acid metabolism resulting from biallelic mutations of GCDH. Without treatment, GA1 causes striatal degeneration in >80% of affected children before two years of age. We analyzed clinical, biochemical, and developmental outcomes for 168 genotypically diverse GA1 patients managed at a single center over 31 years, here separated into three treatment cohorts: children in Cohort I (n = 60; DOB 2006-2019) were identified by newborn screening (NBS) and treated prospectively using a standardized protocol that included a lysine-free, arginine-enriched metabolic formula, enteral l-carnitine (100 mg/kg•day), and emergency intravenous (IV) infusions of dextrose, saline, and l-carnitine during illnesses; children in Cohort II (n = 57; DOB 1989-2018) were identified by NBS and treated with natural protein restriction (1.0-1.3 g/kg•day) and emergency IV infusions; children in Cohort III (n = 51; DOB 1973-2016) did not receive NBS or special diet. The incidence of striatal degeneration in Cohorts I, II, and III was 7%, 47%, and 90%, respectively (p < .0001). No neurologic injuries occurred after 19 months of age. Among uninjured children followed prospectively from birth (Cohort I), measures of growth, nutritional sufficiency, motor development, and cognitive function were normal. Adherence to metabolic formula and l-carnitine supplementation in Cohort I declined to 12% and 32%, respectively, by age 7 years. Cessation of strict dietary therapy altered plasma amino acid and carnitine concentrations but resulted in no serious adverse outcomes. In conclusion, neonatal diagnosis of GA1 coupled to management with lysine-free, arginine-enriched metabolic formula and emergency IV infusions during the first two years of life is safe and effective, preventing more than 90% of striatal injuries while supporting normal growth and psychomotor development. The need for dietary interventions and emergency IV therapies beyond early childhood is uncertain.

The Amish health culture and culturally sensitive health services: An exhaustive narrative review

As the Amish population is growing, researcher and practitioner interest in the Amish health culture is also growing. This is largely due to demand from practitioners for population-specific cultural guidance. Once a small area of study, health-themed publications in Amish studies (n = 246) now account for approximately one-fourth of all peer-reviewed publications, and a sizeable percentage address the health culture, i.e. Amish beliefs, practices, attitudes, decision-making processes, financing, and values. In this article, we provide a first-ever exhaustive narrative review of the Amish health culture literature (addressing Amish health conditions elsewhere). Specifically, we address Amish use of modern medicine, complementary & alternative medicine, cultural norms for birthing and intercourse, support and care for the sick and aged, health knowledge, payment for services, barriers to service access, service provider effectiveness, health programming, and ethical conflicts. Our goal is to organize the literature, synthesize findings, identify orienting perspectives, and clarify research questions and directions. Following our synthesis, we reflect on the current state of Amish health culture research, drawing particular attention to strengths and limitations of the oft-used cultural competency paradigm, and recommending more rigorous social scientific theorization of the Amish health culture.

Population-level assessment of atlas occipitalization in artificially modified crania from pre-Hispanic Peru

Atlas occipitalization (AO) is a spinal anomaly, characterized by the fusion of the first cervical vertebra and occipital bone, with a complex etiology that can arise from congenital and environmental causes. AO has been reported in three regions of pre-Hispanic Peru in skeletal remains with artificial cranial modification (ACM), which involves the use of compression devices to permanently alter cranial shape and may have affected the fusion of the atlas and occipital bone. The aims of this study were to gain insights into AO’s etiology by testing correlations between AO and ACM presence/type and geographic region as well as to characterize morphological variation associated with AO. We investigated the geographic distribution of AO and its potential relationship to ACM in a large sample of human crania from eight coastal and highland regions of pre-Hispanic Peru, held at the Smithsonian’s National Museum of Natural History (n = 608, 1300–1500 CE). Eleven cases of AO were observed in three coastal regions—including two previously unreported regions—at an overall frequency of 1.8%. The frequency of AO did not differ significantly between crania with and without ACM, in general or by type, suggesting that ACM is not an etiological factor that influences AO in this sample. AO was observed at a significantly higher rate in the southern coastal region of Arequipa than in any other region. Genetic, dietary, and epidemiological conditions are evaluated as factors possibly shaping the geographic distribution of AO along the central and southern coasts of Peru.

Newborn Screening for Inherited Metabolic Disorders: Early Identification and Long-Term Care for Patients in the Plain Community, Wisconsin, 2011-2017

The Plain community is the fastest-growing religious minority in Wisconsin. This community has a high incidence of genetic disorders, many of which are identifiable through newborn screening. We describe efforts by the Wisconsin Newborn Screening Program (WNSP) to improve health care in the Plain community by targeting early identification of, and intervention for, patients with inherited metabolic disorders. WNSP formed partnerships with families and health care providers to increase awareness of screening procedures and the intended benefits of screening, modify testing algorithms to enhance detection, and establish medical homes for patients with confirmed disorders. The estimated number of Plain newborns screened increased by 25.5% during the study period, from 547 in 2011 to 736 in 2017; 122 persons underwent carrier testing, and 143 newborns received second-tier testing. From 2014 to 2017, affected patients received 71 metabolic evaluations in their community medical home without travel to major health centers. This article demonstrates how a comprehensive public health program can help increase screening rates, enhance detection, and establish follow-up care in a hard-to-reach religious community. A key lesson learned was the importance of communication among all stakeholders to develop an effective public health program.

Evolutionary genomic dynamics of Peruvians before, during, and after the Inca Empire

Through the Peruvian Genome Project we generate and analyze the genomes of 280 individuals where the majority have >90% Native American ancestry and explore questions at the interface of evolutionary genetics, history, anthropology, and medicine. This is the most extensive sampling of high-coverage Native American and mestizo whole genomes to date. We estimate an initial peopling of Peru was rapid and began by 12,000 y ago. In addition, the mestizo populations exhibit admixture between Native American groups prior to their Spanish admixture and was likely influenced by the Inca Empire and Spanish conquest. Our results address important Native American population history questions and establish a dataset beneficial to address the underrepresentation of Native American ancestry in sequencing studies.

Native Americans from the Amazon, Andes, and coastal geographic regions of South America have a rich cultural heritage but are genetically understudied, therefore leading to gaps in our knowledge of their genomic architecture and demographic history. In this study, we sequence 150 genomes to high coverage combined with an additional 130 genotype array samples from Native American and mestizo populations in Peru. The majority of our samples possess greater than 90% Native American ancestry, which makes this the most extensive Native American sequencing project to date. Demographic modeling reveals that the peopling of Peru began ∼12,000 y ago, consistent with the hypothesis of the rapid peopling of the Americas and Peruvian archeological data. We find that the Native American populations possess distinct ancestral divisions, whereas the mestizo groups were admixtures of multiple Native American communities that occurred before and during the Inca Empire and Spanish rule. In addition, the mestizo communities also show Spanish introgression largely following Peruvian Independence, nearly 300 y after Spain conquered Peru. Further, we estimate migration events between Peruvian populations from all three geographic regions with the majority of between-region migration moving from the high Andes to the low-altitude Amazon and coast. As such, we present a detailed model of the evolutionary dynamics which impacted the genomes of modern-day Peruvians and a Native American ancestry dataset that will serve as a beneficial resource to addressing the underrepresentation of Native American ancestry in sequencing studies.

Long-term outcomes in Amish patients diagnosed with propionic acidemia

Propionic acidemia (PA) occurs at a higher incidence within the Amish; however, sensitivity of newborn screening and its impact on long-term clinical outcomes has not been reported in this population. This study reviewed screening data and health records of 20 Wisconsin Amish patients diagnosed with PA. Newborn screening did not identify all cases; however, early detection did offer appreciable long-term protection from neurological sequelae. This is the first report summarizing PA cases within the Amish.

Caring for the Amish: What Every Anesthesiologist Should Know

The Amish are a relatively isolated group with cultural and religious customs that differ significantly from the mainstream American population. Functioning as tight-knit communities with strong conservative Christian beliefs, the Amish maintain a culture based on intentional separateness from the outside world. Key aspects of Amish life include distinct clothing and behaviors, a unique language, an agrarian lifestyle, limited formal education, nonviolence/nonaggression, and a general lack of modern technology, as exemplified by the use of the traditional horse-and-buggy. The Amish have distinct health care practices, beliefs, and goals, and because of differing genetics and lifestyle, also have a distinct constellation of health and disease characteristics. This article reviews the core beliefs, community and lifestyle, health care beliefs and practices, and health characteristics of this unique and medically challenging population. Generalizable strategies for providing culturally competent care for any such ethnically, socially, or medically unique community are presented.

Medical genetics and genomic medicine in the United States of America. Part 1: history, demographics, legislation, and burden of disease

Medical genetics and genomic medicine in the United States of America. Part 1: history, demographics, legislation, and burden of disease.

Cross-Sectional Survey on Newborn Screening in Wisconsin Amish and Mennonite Communities

Old Order Amish and Mennonites, or Plain populations, are a growing minority in North America with unique health care delivery and access challenges coupled with higher frequencies of genetic disorders. The objective of this study was to determine newborn screening use and attitudes from western Wisconsin Plain communities. A cross-sectional survey, with an overall response rate of 25 %, provided data representing 2010 children. In households with children (n = 297), the rate of newborn screening was 74 % and all children were screened in 40 % of these households. Lack of access to testing was the most common reason for not screening all children and parental age was inversely associated with testing. The majority of respondents reported some or more knowledge of screening, viewed screening as important, and had access to screening in their communities. Households with children who had never received newborn screening (26 %) reported lower frequencies of favorable responses in all categories compared to households that had at least one child screened. The difference in access to newborn screening was less marked between the groups compared to differences on knowledge and consideration of its importance. Moreover, 55 % of households who had never screened any of their children reported being unlikely or unsure of screening any future children. A focus on improving access to newborn screening alongside establishing approaches to change parental perceptions on the importance of newborn screening is necessary for increasing newborn screening in these Plain communities.

Mitochondrial respiratory chain disorders in the Old Order Amish population

The Old Order Amish populations in the US are one of the Plain People groups and are descendants of the Swiss Anabaptist immigrants who came to North America in the early eighteenth century. They live in numerous small endogamous demes that have resulted in reduced genetic diversity along with a high prevalence of specific genetic disorders, many of them autosomal recessive. Mitochondrial respiratory chain deficiencies arising from mitochondrial or nuclear DNA mutations have not previously been reported in the Plain populations. Here we present four different Amish families with mitochondrial respiratory chain disorders. Mutations in two mitochondrial encoded genes leading to mitochondrial respiratory chain disorder were identified in two patients. In the first case, MELAS syndrome caused by a mitochondrial DNA (mtDNA) mutation (m.3243A>G) was identified in an extended Amish pedigree following a presentation of metabolic strokes in the proband. Characterization of the extended family of the proband by a high resolution melting assay identified the same mutation in many previously undiagnosed family members with a wide range of clinical symptoms. A MELAS/Leigh syndrome phenotype caused by a mtDNA mutation [m.13513G>A; p.Asp393Asn] in the ND5 gene encoding the ND5 subunit of respiratory chain complex I was identified in a patient in a second family. Mutations in two nuclear encoded genes leading to mitochondrial respiratory chain disorder were also identified in two patients. One patient presented with Leigh syndrome and had a homozygous deletion in the NDUFAF2 gene, while the second patient had a homozygous mutation in the POLG gene, [c.1399G>A; p.Ala467Thr]. Our findings identify mitochondrial respiratory chain deficiency as a cause of disease in the Old Order Amish that must be considered in the context of otherwise unexplained systemic disease, especially if neuromuscular symptoms are present.

Administration of branched-chain amino acids alters the balance between pro-inflammatory and anti-inflammatory cytokines

Acute leucine intoxication and neurologic deterioration can develop rapidly at any age as a result of net protein degradation precipitated by infection or psychological stress in patients with maple syrup urine disease (MSUD). Here, we investigated the effects of acute and chronic Hyper-BCAA (H-BCAA) administration on pro- and anti-inflammatory cytokines in the brains of rats. For acute administration, Wistar rats (10 and 30 days) received three injections of BCAA pool (15.8 μL/g at 1-h intervals) or saline, subcutaneously. For chronic administration, Wistar rats (7 days) received of BCAA pool or saline twice a day for 21 days, subcutaneously. Our results showed that acute administration of H-BCAA increased IL-1β (∼ 78%; p ≤ 0.009) and TNF-α (∼ 155%; p ≤ 0.026) levels in the cerebral cortex but not in the hippocampus of infant rats. Moreover, IL-6 levels were increased in the hippocampus (∼ 135%; p ≤ 0.009) and cerebral cortex (∼ 417%; p ≤ 0.008), whereas IL-10 levels were decreased only in the hippocampus (∼ 42%; p ≤ 0.009). However, repeated administration of H-BCAA decreased IL-1β (∼ 59%; p ≤ 0.047), IL-6 (∼ 70%; p ≤ 0.009) and IFN-γ (∼ 70%; p ≤ 0.008) levels in the cerebral cortex, whereas the IL-6 (∼ 67%; p ≤ 0.009), IL-10 (∼ 58%; p ≤ 0.01) and IFN-γ (∼ 67%; p ≤ 0.009) levels were decreased in the hippocampus. These findings suggest that a better understanding of the inflammatory response in MSUD patients may be useful to develop therapeutic strategies to modulate the hyperinflammatory/hypoinflammatory axis.

GENLIB: an R package for the analysis of genealogical data

BACKGROUND

Founder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for researchers in evolutionary and population genetics, demography and genetic epidemiology. However, analyzing large genealogical datasets requires specialized methods and software. The GENLIB software was developed to study the large genealogies of the French Canadian population of Quebec, Canada. These genealogies are accessible through the BALSAC database, which contains over 3 million records covering the whole province of Quebec over four centuries. Using this resource, extended pedigrees of up to 17 generations can be constructed from a sample of present-day individuals.

RESULTS

We have extended and implemented GENLIB as a package in the R environment for statistical computing and graphics, thus allowing optimal flexibility for users. The GENLIB package includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations. The goal of this paper is to present the full functionalities of GENLIB. We used a sample of 140 individuals from the province of Quebec (Canada) to demonstrate GENLIB's functions. Ascending genealogies for these individuals were reconstructed using BALSAC, yielding a large pedigree of 41,523 individuals. Using GENLIB's functions, we provide a detailed description of these genealogical data in terms of completeness, genetic contribution of founders, relatedness, inbreeding and the overall complexity of the genealogical tree. We also present gene-dropping simulations based on the whole genealogy to investigate identical-by-descent sharing of alleles and chromosomal segments of different lengths and estimate probabilities of identical-by-descent sharing.

CONCLUSIONS

The R package GENLIB provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.

Byler disease: early natural history

OBJECTIVES

Byler disease, originally described in Amish kindred, results from mutations in ATPase Class I Type 8b Member 1 (ATP8b1). Specific clinical reports of Amish Byler disease were last published 40 years ago. These investigations were directed at the present detailed clinical understanding of the early course of hepatic manifestations of Byler disease.

METHODS

This study analyzed routine clinical practice and outcomes of children with Byler disease (defined by homozygous c.923G>T mutation in ATP8b1), who initially presented to Children's Hospital of Pittsburgh of UPMC between January 2007 and October 2014. Data were analyzed to the earlier of 24 months of age or partial external biliary diversion.

RESULTS

Six children presented between 1 and 135 days of life: 2 presented with newborn direct hyperbilirubinemia, 2 had complications of coagulopathy, 1 had failure to thrive and rickets, and 1 sibling was identified by newborn genetic testing. Intensive fat-soluble vitamin supplementation was required to prevent insufficiencies in vitamins D, E, and K. Hyperbilirubinemia was variable both over time and between children. Serum bile acid levels were elevated, whereas γ-glutamyltranspeptidase levels were low normal. Scratching behavior (pruritus) was intractable in 4 of 6 children with onset between 6 and 12 months of age. Features of portal hypertension were not observed. Partial external biliary diversion was used during the second year of life in 4 children.

CONCLUSIONS

Detailed analysis of Byler disease revealed varied disease presentation and course. Nutritional issues and pruritus dominated the clinical picture in the first 2 years of life.

History and current status of newborn screening for severe combined immunodeficiency

The development of a T-cell receptor excision circle (TREC) assay utilizing dried blood spots in universal newborn screening has allowed the early detection of T-cell lymphopenia in newborns. Diagnosis of severe combined immunodeficiency (SCID) in affected infants in the neonatal period, while asymptomatic, permits early treatment and restoration of a functional immune system. SCID was the first immunodeficiency disease to be added to the Recommended Uniform Screening Panel of Core Conditions in the United States in 2010, and it is now implemented in 26 states in the U.S. This review covers the development of newborn screening for SCID, the biology of the TREC test, its current implementation in the U.S., new findings for SCID in the newborn screening era, and future directions.

Ethnicity and Geographic Distribution of Pediatric Chronic Ataxia in Manitoba

Background:

Genetic and environmental factors are important determinants of disease distribution. Several disorders associated with ataxia are known to occur more commonly in certain ethnic groups; for example, the disequilibrium syndrome in the Hutterites. The aim of this study was to determine the ethnic and geographic distribution of pediatric patients with chronic ataxia in Manitoba, Canada.

Methods:

We identified 184 patients less than 17 years-of-age with chronic ataxia during 1991-2008 from multiple sources. Their diagnosis, ethnicity and place of residence were determined following a chart review.

Results:

Most patients resided in Manitoba (N=177) and the majority in Winnipeg, the provincial capital. Thirty five Aboriginal, 29 Mennonite and 11 Hutterite patients resided in Manitoba. The latter two groups were significantly overrepresented in our cohort. Ataxia telangiectasia, mitochondrial disorders, and non-progressive ataxia of unknown etiology associated with pyramidal tracts signs and developmental delay were significantly more common in Mennonite patients. Four of five patients with neuronal migration disorders associated with chronic ataxia were Aboriginal. Few isolated disorders with chronic ataxia occurred in the 11 Hutterite patients including a Joubert syndrome related disorder.

Conclusions:

Three disorders associated with chronic ataxia were more prevalent than expected in Mennonites in Manitoba. Few rare disorders were more prevalent in the Hutterite and Aboriginal population. Further research is needed to determine the risk factors underlying these variations in prevalence within different ethnic groups. The unique risk factor profiles of each ethnic group need to be considered in health promotion endeavors.

Primary ciliary dyskinesia-causing mutations in Amish and Mennonite communities

OBJECTIVE

To determine whether individuals with primary ciliary dyskinesia (PCD) from unrelated Amish and Mennonite families harbor a single and unique founder mutation.

STUDY DESIGN

Subjects from Amish and Mennonite communities in several states were enrolled in the study. All subjects were clinically characterized, and nasal nitric oxide levels were measured. Nasal epithelial scrapings were collected from several subjects for ciliary ultrastructural analyses. DNA was isolated from patients with PCD and their unaffected first- and second-degree relatives. Genome-wide homozygosity mapping, linkage analyses, targeted mutation analyses, and exome sequencing were performed.

RESULTS

All subjects from Old-Order Amish communities from Pennsylvania were homozygous for a nonsense mutant DNAH5 allele, c.4348C>T (p.Q1450X). Two affected siblings from an unrelated Mennonite family in Arkansas were homozygous for the same nonsense DNAH5 mutation. Children with PCD from an Amish family from Wisconsin had biallelic DNAH5 mutations, c.4348C>T (p.Q1450X) and c.10815delT (p.P3606HfsX23), and mutations in other genes associated with PCD were also identified in this community.

CONCLUSION

The Amish and Mennonite subjects from geographically dispersed and socially isolated communities had the same founder DNAH5 mutation, owing to the common heritage of these populations. However, disease-causing mutations in other PCD-associated genes were also found in affected individuals in these communities, illustrating the genetic heterogeneity in this consanguineous population.

Whole-exome capture and sequencing identifies HEATR2 mutation as a cause of primary ciliary dyskinesia

Motile cilia are essential components of the mucociliary escalator and are central to respiratory-tract host defenses. Abnormalities in these evolutionarily conserved organelles cause primary ciliary dyskinesia (PCD). Despite recent strides characterizing the ciliome and sensory ciliopathies through exploration of the phenotype-genotype associations in model organisms, the genetic bases of most cases of PCD remain elusive. We identified nine related subjects with PCD from geographically dispersed Amish communities and performed exome sequencing of two affected individuals and their unaffected parents. A single autosomal-recessive nonsynonymous missense mutation was identified in HEATR2, an uncharacterized gene that belongs to a family not previously associated with ciliary assembly or function. Airway epithelial cells isolated from PCD-affected individuals had markedly reduced HEATR2 levels, absent dynein arms, and loss of ciliary beating. MicroRNA-mediated silencing of the orthologous gene in Chlamydomonas reinhardtii resulted in absent outer dynein arms, reduced flagellar beat frequency, and decreased cell velocity. These findings were recapitulated by small hairpin RNA-mediated knockdown of HEATR2 in airway epithelial cells from unaffected donors. Moreover, immunohistochemistry studies in human airway epithelial cells showed that HEATR2 was localized to the cytoplasm and not in cilia, which suggests a role in either dynein arm transport or assembly. The identification of HEATR2 contributes to the growing number of genes associated with PCD identified in both individuals and model organisms and shows that exome sequencing in family studies facilitates the discovery of novel disease-causing gene mutations.

One community's effort to control genetic disease

In 1989, we established a small community health clinic to provide care for uninsured Amish and Mennonite children with genetic disorders. Over 20 years, we have used publicly available molecular data and sophisticated technologies to improve diagnostic efficiency, control laboratory costs, reduce hospitalizations, and prevent major neurological impairments within a rural underserved community. These actions allowed the clinic's 2010 operating budget of $1.5 million to save local communities an estimated $20 to $25 million in aggregate medical costs. This exposes an unsettling fact: our failure to improve the lot of most people stricken with genetic disease is no longer a matter of scientific ignorance or prohibitive costs but of choices we make about how to implement existing knowledge and resources.

Is Race Determination in the Medicolegal Setting Important?

Racial designations have evolved over the years to accommodate the changes in our population demographics. The Federal Office of Management and Budget (OMB) has developed Federal Standards to assist with the uniform documentation and reporting of race and ethnicity. A minimum of five defined categories currently exist for race (American Indian or Alaska Native, Asian, Black or African American, Native Hawaiian or Other Pacific Islander and White). Ethnicity is separated into either Hispanic origin or Non-Hispanic origin. Current death certificates allow for the selection of one or more races; however, only one ethnicity may be chosen. Race of unknown decedents is either based subjectively on the observer's opinion or, in severely decomposed or skeletal remains, by anthropological analysis utilizing sound statistical methodology. If the data and statistical analysis suggest a good classification, the race determination will be correct more often than not. Information obtained from the National Missing and Unidentified Persons System (NamUs) indicates that absence of race determination does not hinder the identification potential. Mortality rates, life expectancy, disease risk and causes of death are often disaggregated by race and/or ethnicity. Differences in the presentation, etiology and outcomes of many diseases have been based on race and ethnicity data. Uniform collection of this data is the key to its importance. Medical examiners, coroners and others tasked with examination of decedents should utilize the defined categories set forth in the OMB Revised Standards for race and ethnicity documentation.

Personalized medicine: ethics for clinical trials

Modern ethical codes in medicine were developed following World War II to provide respect for persons, beneficence, and justice in clinical research. Clinical trial medicine involves greater scrutiny than most research activities. In every instance, clinical trials have institutional review boards to ensure the medical procedure under study complies with regulatory requirements, privacy, informed consent, good practices, safety monitoring, adverse events reporting, and is free of conflicting interests. Mandatory training in medical ethics for all clinical staff is becoming more common, and at some institutions, knowledgeable patient advocates play a watchdog role. In personalized medicine, each patient becomes a clinical trial of one, based on the uniqueness of the person's illness and the relatively tailored treatment. These features imply a shared responsibility between the patient and the researchers because uncertainty exists over the outcome for each individual patient. This chapter introduces ethical considerations using case studies, with historical context, and describes general ethical guidelines for initiating a clinical trial.

Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon

Cultural expansions, including of religions, frequently leave genetic traces of differentiation and in-migration. These expansions may be driven by complex doctrinal differentiation, together with major population migrations and gene flow. The aim of this study was to explore the genetic signature of the establishment of religious communities in a region where some of the most influential religions originated, using the Y chromosome as an informative male-lineage marker. A total of 3139 samples were analyzed, including 647 Lebanese and Iranian samples newly genotyped for 28 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y chromosome. Genetic organization was identified by geography and religion across Lebanon in the context of surrounding populations important in the expansions of the major sects of Lebanon, including Italy, Turkey, the Balkans, Syria, and Iran by employing principal component analysis, multidimensional scaling, and AMOVA. Timing of population differentiations was estimated using BATWING, in comparison with dates of historical religious events to determine if these differentiations could be caused by religious conversion, or rather, whether religious conversion was facilitated within already differentiated populations. Our analysis shows that the great religions in Lebanon were adopted within already distinguishable communities. Once religious affiliations were established, subsequent genetic signatures of the older differentiations were reinforced. Post-establishment differentiations are most plausibly explained by migrations of peoples seeking refuge to avoid the turmoil of major historical events.

PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County

BACKGROUND

Because they are a closed founder population, the Old Order Amish (OOA) of Lancaster County have been the subject of many medical genetics studies. We constructed four versions of Anabaptist Genealogy Database (AGDB) using three sources of genealogies and multiple updates. In addition, we developed PedHunter, a suite of query software that can solve pedigree-related problems automatically and systematically.

METHODS

We report on how we have used new features in PedHunter to quantify the number and expected genetic contribution of founders to the OOA. The queries and utility of PedHunter programs are illustrated by examples using AGDB in this paper. For example, we calculated the number of founders expected to be contributing genetic material to the present-day living OOA and estimated the mean relative founder representation for each founder. New features in PedHunter also include pedigree trimming and pedigree renumbering, which should prove useful for studying large pedigrees.

RESULTS

With PedHunter version 2.0 querying AGDB version 4.0, we identified 34,160 presumed living OOA individuals and connected them into a 14-generation pedigree descending from 554 founders (332 females and 222 males) after trimming. From the analysis of cumulative mean relative founder representation, 128 founders (78 females and 50 males) accounted for over 95% of the mean relative founder contribution among living OOA descendants.

DISCUSSION/CONCLUSIONS

The OOA are a closed founder population in which a modest number of founders account for the genetic variation present in the current OOA population. Improvements to the PedHunter software will be useful in future studies of both the OOA and other populations with large and computerized genealogies.

Classical maple syrup urine disease and brain development: principles of management and formula design

Branched-chain ketoacid dehydrogenase deficiency results in complex and volatile metabolic derangements that threaten brain development. Treatment for classical maple syrup urine disease (MSUD) should address this underlying physiology while also protecting children from nutrient deficiencies. Based on a 20-year experience managing 79 patients, we designed a study formula to (1) optimize transport of seven amino acids (Tyr, Trp, His, Met, Thr, Gln, Phe) that compete with branched-chain amino acids (BCAAs) for entry into the brain via a common transporter (LAT1), (2) compensate for episodic depletions of glutamine, glutamate, and alanine caused by reverse transamination, and (3) correct deficiencies of omega-3 essential fatty acids, zinc, and selenium widespread among MSUD patients. The formula was enriched with LAT1 amino acid substrates, glutamine, alanine, zinc, selenium, and alpha-linolenic acid (18:3n-3). Fifteen Old Order Mennonite children were started on study formula between birth and 34 months of age and seen at least monthly in the office. Amino acid levels were checked once weekly and more often during illnesses. All children grew and developed normally over a period of 14-33 months. Energy demand, leucine tolerance, and protein accretion were tightly linked during periods of normal growth. Rapid shifts to net protein degradation occurred during illnesses. At baseline, most LAT1 substrates varied inversely with plasma leucine, and their calculated rates of brain uptake were 20-68% below normal. Treatment with study formula increased plasma concentrations of LAT1 substrates and normalized their calculated uptakes into the nervous system. Red cell membrane omega-3 polyunsaturated fatty acids and serum zinc and selenium levels increased on study formula. However, selenium and docosahexaenoic acid (22:6n-3) levels remained below normal. During the study period, hospitalizations decreased from 0.35 to 0.14 per patient per year. There were 28 hospitalizations managed with MSUD hyperalimentation solution; 86% were precipitated by common infections, especially vomiting and gastroenteritis. The large majority of catabolic illnesses were managed successfully at home using 'sick-day' formula and frequent amino acid monitoring. We conclude that the study formula is safe and effective for the treatment of classical MSUD. In principle, dietary enrichment protects the brain against deficiency of amino acids used for protein accretion, neurotransmitter synthesis, and methyl group transfer. Although the pathophysiology of MSUD can be addressed through rational formula design, this does not replace the need for vigilant clinical monitoring, frequent measurement of the complete amino acid profile, and ongoing dietary adjustments that match nutritional intake to the metabolic demands of growth and illness.

Genetics, medicine, and the Plain people

The Old Order Amish and Old Order Mennonite populations of Pennsylvania are descended from Swiss Anabaptist immigrants who came to the New World in the early eighteenth century. Today they live in many small endogamous demes across North America. Genetically, these demes have dissimilar allele frequencies and disease spectra owing to unique founders. Biological and social aspects of Old Order communities make them ideal for studies in population genetics and genomic medicine, and over the last 40 years, advances in genomic science coincided with investigational studies in Plain populations. Newer molecular genetic technologies are sufficiently informative, rapid, and flexible to use in a clinical setting, and we have successfully integrated these tools into a rural pediatric practice. Our studies with the Pennsylvania Plain communities show that population-specific genetic knowledge provides a powerful framework in which to prevent disease, reduce medical costs, and create new insights into human biology.

Care for Amish and Mennonite children with cystic fibrosis: a case series

BACKGROUND

Published articles have described a lack of willingness to allow preventative measures, as well as other types of modern therapies, as an obstacle to providing medical care for Amish and Mennonite populations.

METHODS

We present data regarding the 12 Amish and Mennonite patients at the SUNY Upstate Medical University Pediatric Cystic Fibrosis Center and three representative case reports.

RESULTS

Families of patients from these communities receiving care at our Center have accepted preventive therapy, acute medical interventions including home intravenous antibiotic administration, and some immunizations for their children with cystic fibrosis, which have improved the health of our patients. Some have even participated in clinical research trials. Health care education for both the child and family is warranted and extensive. Significant Cystic Fibrosis Center personnel time and fundraising are needed in order to address medical bills incurred by uninsured Amish and Mennonite patients.

CONCLUSION

Amish and Mennonite families seeking care for cystic fibrosis may choose to utilize modern medical therapies for their children, with resultant significant improvement in outcome.

Unique disease heritage of the Dutch-German Mennonite population

The Dutch-German Mennonites are a religious isolate with foundational roots in the 16th century. A tradition of endogamy, large families, detailed genealogical records, and a unique disease history all contribute to making this a valuable population for genetic studies. Such studies in the Dutch-German Mennonite population have already contributed to the identification of the causative genes in several conditions such as the incomplete form of X-linked congenital stationary night blindness (CSNB2; previously iCSNB) and hypophosphatasia (HOPS), as well as the discovery of founder mutations within established disease genes (MYBPC1, CYP17alpha). The Dutch-German Mennonite population provides a strong resource for gene discovery and could lead to the identification of additional disease genes with relevance to the general population. In addition, further research developments should enhance delivery of clinical genetic services to this unique community. In the current review we discuss 31 genetic conditions, including 17 with identified gene mutations, within the Dutch-German Mennonite population.

Homozygosity for a novel splice site mutation in the cardiac myosin-binding protein C gene causes severe neonatal hypertrophic cardiomyopathy

Hypertrophic cardiomyopathy is typically inherited in an autosomal dominant pattern and has a variable age of onset and prognosis. Mutations in the myosin-binding protein C (MYBPC3) gene are one of the most frequent genetic causes of the disease. Patients with MYBPC3 mutations generally have a late onset and a relatively good prognosis. We report here more than 20 Old Order Amish children with severe neonatal hypertrophic cardiomyopathy caused by a novel homozygous splice site mutation in the MYBPC3 gene. The affected children typically presented with signs and symptoms of congestive heart failure during the first 3 weeks of life. Echocardiography revealed hypertrophic non-obstructive cardiomyopathy. These children had a life span averaging 3-4 months. All patients died from heart failure before 1 year of age unless they received a heart transplant. A genome-wide mapping study was performed in three patients. The disease related gene was localized to a 4.6 Mb region on chromosome 11p11.2-p11.12. This homozygous block contained MYBPC3, a previously identified cardiomyopathy related gene. We identified a novel homozygous mutation, c.3330 + 2T > G, in the splice-donor site of MYBPC3 intron 30. The mutation resulted in skipping of the 140-bp exon 30, which led to a frame shift and premature stop codon in exon 31 (p.Asp1064GlyfsX38). We have found a substantial incidence of this phenotype in Old Order Amish communities. It is also concerning that many unidentified heterozygous individuals who are at risk for development of hypertrophic cardiomyopathy do not receive proper medical attention in the communities.

Multimodal imaging of striatal degeneration in Amish patients with glutaryl-CoA dehydrogenase deficiency

Despite early diagnosis, one-third of Amish infants with glutaryl-CoA dehydrogenase deficiency (GA1) develop striatal lesions that leave them permanently disabled. To better understand mechanisms of striatal degeneration, we retrospectively studied imaging results from 25 Amish GA1 patients homozygous for 1296C>T mutations in GCDH. Asymptomatic infants had reduced glucose tracer uptake and increased blood volume throughout gray matter, which may signify a predisposition to brain injury. Nine children (36%) developed striatal lesions: three had sudden motor regression during infancy whereas six had insidious motor delay associated with striatal lesions of undetermined onset. Acute striatal necrosis consisted of three stages: (1) an acute stage, within 24 h of motor regression, characterized by cytotoxic oedema within the basal ganglia, cerebral oligemia, and rapid transit of blood throughout gray matter; (2) a sub-acute stage, 4-5 days after the onset of clinical signs, characterized by reduced striatal perfusion and glucose uptake, and supervening vasogenic oedema; and (3) a chronic stage of striatal atrophy. Apparent diffusion coefficient maps revealed that at least two of the six patients with insidious motor delay suffered striatal injuries before or shortly after birth, followed by latent periods of several months before disability was apparent. Thus, acute and insidious presentations may occur by similar mechanisms, and differ only with regard to the timing of injury. Intravenous fluid and dextrose therapy for illnesses during the first 2 years of life was the only intervention that was clearly neuroprotective in this cohort (odds ratio for brain injury = 0.04, 95% confidence interval = 0.01-0.34; P < 0.001).

Health status, health conditions, and health behaviors among Amish women. Results from the Central Pennsylvania Women's Health Study (CePAWHS)

We performed one of the first systematic, population-based surveys of women in Amish culture. We used these data to examine health status and health risks in a representative sample of 288 Amish women ages 18-45 living in Lancaster County, Pennsylvania, in particular for risks associated with preterm and low birthweight infants, compared with a general population sample of 2,002 women in Central Pennsylvania. Compared with women in the general population, Amish women rated their physical health approximately at the same level, but reported less stress, fewer symptoms of depression, and had higher aggregate scores for mental health. Amish women reported low levels of intimate partner violence, high levels of social support, and they perceived low levels of unfair treatment owing to gender compared with the general population. Amish women also reported higher fertility, fewer low birthweight babies, but the same number of preterm births as the general population. The findings suggest that these outcomes may be due to higher levels of social support and better preconceptional behavior among Amish women.

A nonsense mutation of PEPD in four Amish children with prolidase deficiency

Encoded by the peptidase D (PEPD) gene located at 19q12-q13.11, prolidase is a ubiquitous cytosolic enzyme that catalyzes hydrolysis of oligopeptides with a C-terminal proline or hydroxyproline. We describe here four Amish children with a severe phenotype of prolidase deficiency in the Geauga settlements of Ohio as the first report of prolidase deficiency in the Amish population as well as in the United States. The patients presented with infection, hepatosplenomegaly, or thrombocytopenia, in contrast to most cases previously reported in the literature, presenting with skin ulcers. All four patients had typical facial features, classic skin ulcers, and multisystem involvement. Recurrent infections, asthma-like chronic reactive airway disease, hyperimmunoglobulins, hepatosplenomegaly with mildly elevated aspartate transaminase (AST), anemia, and thrombocytopenia were common and massive imidodipeptiduria was universal. Prolidase activity in our patients is nearly undetectable. Direct sequencing of PCR-amplified genomic DNA for all of the exons from the four patients revealed the same homozygous single nucleotide mutation c.793 T > C in exon 11, resulting in a premature stop-codon at amino acid residue 265 (p.R265X). It is speculated that the severe phenotype in these patients might be associated with the type of the PEPD gene mutation.