Early child health in Lahore, Pakistan: II. Inbreeding

Metabolomics of a neonatal cohort from the Alliance for Maternal and Newborn Health Improvement biorepository: Effect of preanalytical variables on reference intervals

BACKGROUND

The study was conducted to determine reference interval (RI) and evaluate the effect of preanalytical variables on Dried blood spot (DBS)-amino acids, acylcarnitines and succinylacetone of neonates.

METHODOLOGY

DBS samples were collected within 48-72 hours of life. Samples were analyzed for biochemical markers on tandem mass spectrometer at the University of Iowa. Comparison of RI across various categorical variables were performed.

RESULTS

A total of 610 reference samples were selected based on exclusion criteria; 53.2% being females. Mean gestational age (GA) of mothers at the time of delivery was 38.7±1.6 weeks; 24.5% neonates were of low birth weight and 14.3% were preterm. Out of the total 610 neonates, 23.1% were small for GA. Reference intervals were generated for eleven amino acids, thirty-two acylcarnitines and succinylacetone concentrations. Markers were evaluated with respect to the influence of gender, GA, weight and time of sampling and statistically significant minimal differences were observed for some biomarkers.

CONCLUSION

RI for amino acids, succinylacetone and acylcarnitine on DBS has been established for healthy neonates, which could be of use in the clinical practice. Clinically significant effect of GA, weight, gender and time of sampling on these markers were not identified.

Implementation of public health genomics in Pakistan

There has been considerable recent progress in the implementation of public health genomics policy throughout the developed world. However, in the developing world, genetic services still remain limited, or unavailable to most. Here, we discuss challenges and opportunities related to the implementation of public health genomics in developing countries. We focus on Pakistan, a country with one of the world's highest rates of inter-family marriages and prevalence of inherited genetic conditions. Pakistan still lacks a national newborn screening programme, clinical genetic testing services, or public health genomics framework. The medical infrastructure in Pakistan, characterized by limited publicly-funded health services and a significant burden of infectious disease, may contribute to de-prioritization of genetic health services. In addition, there are a number of societal, cultural and religious factors to consider. Recently a number of large research studies have been conducted in populations of Pakistani descent, mostly in collaboration with major US, UK and European institutions. Some of these have yielded high-impact scientific findings, but have yet to translate into public health outcomes in Pakistan. Before the benefits of genomics can be realized in developing countries, the first initial steps towards strategic prioritization, resourcing, and long-term goal setting are required. We propose some practical recommendations and possible first steps forward.

Ambiguous genitalia: An overview of 7 years experience at the Children's Hospital & Institute of Child Health, Lahore, Pakistan

Objective:

To determine the classification and etiological diagnosis of children presented with ambiguous genitalia/atypical genitalia according to the newer classification system of Disorder of Sex Development (DSD).

Methods:

This observational, cross-sectional study was conducted at the Department of Pediatric Endocrinology and Diabetes at The Children’s Hospital &Institute of Child Health, Lahore from January, 2007 to December; 2014. Files of all the children with ambiguous genitalia were retrospectively analyzed and relevant data was retrieved. All the information was recorded on predesigned proforma and analyzed accordingly.

Results:

A total of 300 cases of ambiguous genitalia classified according to the new DSD classification. 46, XX DSD were 54.3% (n=163), 46, XY DSD were 43.7% (n=131), sex chromosome DSD were 2% (n=6). Among 46, XX DSD cases, the most common cause was congenital adrenal hyperplasia (97%, n=158). However, in 46, XY DSD partial androgen insensitivity/5α-reductase deficiency (62%. n=81) constituted the most commonest disorder. Other causes of 46XY DSD include testosterone synthesis defect(23%), congenital adrenal hyperplasia (CAH,12%), testis regression syndrome (1.5%) and persistent mullerian duct syndrome (PMDS,1.5%). Sex chromosome disorder constituted one case of iso-chromosome X turner syndrome, mixed gonadal dysgenesis (n=3), ovotesticular DSD/chimerism (n=2).

Conclusion:

Ambiguous genitalia have varied etiologies, 46; XXDSD found being the commonest of all, showing predominance of CAH especially salt loosing type. The early detection and prompt treatment of cases of ambiguous genitalia plays a pivotal role in the management of acute life threatening condition and gender assignment.

The Geographic Origins of Ethnic Groups in the Indian Subcontinent: Exploring Ancient Footprints with Y-DNA Haplogroups

Several studies have evaluated the movements of large populations to the Indian subcontinent; however, the ancient geographic origins of smaller ethnic communities are not clear. Although historians have attempted to identify the origins of some ethnic groups, the evidence is typically anecdotal and based upon what others have written before. In this study, recent developments in DNA science were assessed to provide a contemporary perspective by analyzing the Y chromosome haplogroups of some key ethnic groups and tracing their ancient geographical origins from genetic markers on the Y-DNA haplogroup tree. A total of 2,504 Y-DNA haplotypes, representing 50 different ethnic groups in the Indian subcontinent, were analyzed. The results identified 14 different haplogroups with 14 geographic origins for these people. Moreover, every ethnic group had representation in more than one haplogroup, indicating multiple geographic origins for these communities. The results also showed that despite their varied languages and cultural differences, most ethnic groups shared some common ancestors because of admixture in the past. These findings provide new insights into the ancient geographic origins of ethnic groups in the Indian subcontinent. With about 2,000 other ethnic groups and tribes in the region, it is expected that more scientific discoveries will follow, providing insights into how, from where, and when the ancestors of these people arrived in the subcontinent to create so many different communities.

Y-STR Haplogroup Diversity in the Jat Population Reveals Several Different Ancient Origins

The Jats represent a large ethnic community that has inhabited the northwest region of India and Pakistan for several thousand years. It is estimated the community has a population of over 123 million people. Many historians and academics have asserted that the Jats are descendants of Aryans, Scythians, or other ancient people that arrived and lived in northern India at one time. Essentially, the specific origin of these people has remained a matter of contention for a long time. This study demonstrated that the origins of Jats can be clarified by identifying their Y-chromosome haplogroups and tracing their genetic markers on the Y-DNA haplogroup tree. A sample of 302 Y-chromosome haplotypes of Jats in India and Pakistan was analyzed. The results showed that the sample population had several different lines of ancestry and emerged from at least nine different geographical regions of the world. It also became evident that the Jats did not have a unique set of genes, but shared an underlying genetic unity with several other ethnic communities in the Indian subcontinent. A startling new assessment of the genetic ancient origins of these people was revealed with DNA science.

Etiology and genetic factors in clefts of lip and/or palate reported at children's hospital, Lahore, Pakistan

The etiology of cleft lip (CL) and/or cleft palate (CP) has been extensively studied in industrialized countries and is suggested to be heterogeneous with increasing evidence that both genetic and environmental factors are operating. To evaluate this assertion in a developing country like Pakistan, a case finding cross-sectional study was completed from 1^st July 2010 to 31^st May 2011 for 100 cases of CL and/or CP referred to the Genetic Clinic of the Children’s Hospital, Lahore, Pakistan. A clinical examination followed by necessary diagnostic work-up was completed for each case. The cause of CL and/or CP was clear in 18% of the children (n = 18). Environmental causes were found in 6 children (four mothers developed hyperthermia during the 2^nd month of gestation, one mother was diabetic, and one mother was a known case of epilepsy and took sodium valproate throughout her pregnancy). Six children were suffering from known genetic malformation syndromes (each with Jarcho-Levin syndrome, Oral-Facial-Digital syndrome type XI, Oral-Duplication syndrome, Kabuki syndrome, Fronto-nasal dysplasia and Nager syndrome). Novel chromosomal aberrations were identified in 2 children. In 82% of the children (n = 82) the cause of oro-facial clefts remained unknown. Impact of gender and consanguinity on the development of CL and/or CP was also studied. Prevalence of CP was significantly more among female children as compared to that in males (P < 0.05). Associated anomalies were present in 18% of the cases, anomalies of the craniofacial region being the most common. These findings were compared with regional and international studies.

An empirical analysis of the effects of consanguineous marriages on economic development

In this study, development experiences toward economic development are investigated to provide an alternative analysis of economic development, human capital, and genetic inheritance in the light of consanguineous marriages. The countries analyzed in the study are discussed in accordance with consanguineous marriage practices and classified by their per capita gross domestic product (GDP) growth. A broad range of countries are analyzed in the study. Arab countries that experienced high rates of growth in their gross national income during the twentieth century but failed to fulfill adequate development measures as reflected in the growth in national income, countries undergoing transition from tight government regulation to free market democracy, and African nations that have experienced complications in the process of development show important differences in the process of economic development. It is shown that the countries that have reached high average development within the context of per capita GDP have overcome problems integral to consanguineous marriage.

The effect of religious, cultural and social identity on population genetic structure among Muslims in Pakistan

Knowledge of historical demography and contemporary social stratification can be valuable in understanding disease patterns, including genetic disorders, especially in communities that have a high prevalence of endogamous and/or consanguineous marriages. This paper provides a background to the religious, historical and socio-cultural factors that have helped define the bounds of endogamy for Muslims in undivided India and more specifically since the creation of Pakistan. The preference for endogamous marriage is based on the clan-oriented nature of the society, which values and actively seeks similarities in social group identity based on several factors, including religious, sectarian, ethnic, and tribal/clan affiliation. Religious affiliation is itself multi-layered and includes religious considerations other than being Muslim, such as sectarian identity (e.g. Shia or Sunni, etc.) and religious orientation within the sect (Isnashari, Ismaili, Ahmedi, etc.). Both ethnic affiliation (e.g. Sindhi, Baloch, Punjabi, etc.) and membership of specific biraderis or zat/quoms are additional integral components of social identity. Within the bounds of endogamy defined by the above parameters, close consanguineous unions are preferential due to a congruence of key features of group- and individual-level background factors.

Prevalence and aetiology of congenital birth defects, infant mortality and mental retardation in Lahore, Pakistan: a prospective cohort study

AIM

To study the health and development of children in a developing and low-income country.

METHODS

The health and development of children in Lahore in northern Pakistan have been studied since 1981 in a collaborative project between Pakistani and Swedish university institutions and the Swedish Agency for Research Cooperation with Developing Countries (SAREC). The study described in this paper comprised four different areas in Lahore with different degrees of urbanization and different social conditions. All pregnancies in the four areas were registered during the period March 1984 to July 1986 and were followed up from the 5th month of pregnancy. All 1476 children born after 1 September 1984 were followed up from birth to 12 y of age.

RESULTS

The perinatal mortality in the whole material was 5.4%. It was highest in the periurban slum (7.5%) and lowest in the upper-middle class cohort (3.3%). Overall infant mortality was 10%. It was highest (14%) in the periurban slum and lowest (2%) in the upper-middle class group. Overall incidence of serious birth defects was 5%. It was highest in the periurban slum community (7%) and lowest in the upper-middle class cohort (3%). The overall cumulative incidence of severe mental retardation per 100 live births was 1.1. It was highest (2.2) in the periurban slum and lowest (0.4) in the upper-middle class group. The overall prevalence of mild mental retardation among 6-10-y-old children was 6.2 per 100. It was highest in the periurban slum (10.5) and lowest (1.3 per 100) in the upper-middle class group. Poverty, malnutrition, birth trauma and consanguinity were common causes of infant mortality and mental retardation in Lahore, Pakistan.

CONCLUSION

Preventive measures with provision of obstetric and health services, services for genetic information and risk evaluation, vaccination programmes and identification of children with retarded development for specific stimulation and habilitation measures, e.g. organized play activities, are important in developing and low-income countries.

Congenital heart disease and associated malformations in children with cleft lip and palate in Pakistan

Children with cleft lip and palate often have other associated malformations. The reported incidence and types of associated malformations vary between different studies. There is a great paucity of literature on the subject from the region in general and none from Pakistan at all. The purpose of this study was to assess the frequency of associated malformations, particularly congenital heart disease, in children with cleft lip and palate presenting to the Aga Khan University (AKU) and Murshid Hospital (MH). From 1st October 1999 to 31st March 2002, all children with cleft lip and palate who presented to AKU and MH were prospectively enrolled in the study group. Socio-demographic characteristics and a number of other variables were documented. All children underwent a thorough clinical examination and an echocardiogram as part of the study protocol. 123 children formed the study group. Thirty-five (29%) of these children were found to have associated malformations. The most common of these was congenital heart disease, which accounted for 51% of all associated malformations. Thirty percent of cleft palate children had associated anomalies while 27% of cleft lip, with or without cleft palate, children had associated anomalies. There was a significant association between children born of a consanguineous marriage and the risk of associated malformations (p-value: 0.001). Consanguinity was present in 74% of children with associated anomalies as compared to 40% of children with no associated anomaly. Dysmorphic features and the presence of associated anomalies were also significantly associated (p-value: 0.009). Dysmorphic features were present in 46% of children with anomalies as compared to 21% of children with no associated anomaly. Fifty percent of children with associated anomalies had a low birth weight compared to 34% of children with no anomalies, but the difference was not statistically significant. The presence of consanguinity in a child with dysmorphic features should raise the suspicion of an associated anomaly. The likelihood of this being a cardiac defect is high and should be ruled out with a thorough clinical examination, supplemented with an echocardiogram in certain cases.

Contribution of BRCA1 and BRCA2 mutations to breast and ovarian cancer in Pakistan

The population of Pakistan has been reported to have the highest rate of breast cancer of any Asian population (excluding Jews in Israel) and one of the highest rates of ovarian cancer worldwide. To explore the contribution that genetic factors make to these high rates, we have conducted a case-control study of 341 case subjects with breast cancer, 120 case subjects with ovarian cancer, and 200 female control subjects from two major cities of Pakistan (Karachi and Lahore). The prevalence of BRCA1 or BRCA2 mutations among case subjects with breast cancer was 6.7% (95% confidence interval [CI] 4.1%-9.4%), and that among case subjects with ovarian cancer was 15.8% (95% CI 9.2%-22.4%). Mutations of the BRCA1 gene accounted for 84% of the mutations among case subjects with ovarian cancer and 65% of mutations among case subjects with breast cancer. The majority of detected mutations are unique to Pakistan. Five BRCA1 mutations (2080insA, 3889delAG, 4184del4, 4284delAG, and IVS14-1A-->G) and one BRCA2 mutation (3337C-->T) were found in multiple case subjects and represent candidate founder mutations. The penetrance of deleterious mutations in BRCA1 and BRCA2 is comparable to that of Western populations. The cumulative risk of cancer to age 85 years in female first-degree relatives of BRCA1-mutation-positive case subjects was 48% and was 37% for first-degree relatives of the BRCA2-mutation-positive case subjects. A higher proportion of case subjects with breast cancer than of control subjects were the progeny of first-cousin marriages (odds ratio [OR] 2.1; 95% CI 1.4-3.3; P=.001). The effects of consanguinity were significant for case subjects with early-onset breast cancer (age <40 years) (OR=2.7; 95% CI 1.5-4.9; P=.0008) and case subjects with ovarian cancer (OR=2.4; 95% CI 1.4-4.2; P=.002). These results suggest that recessively inherited genes may contribute to breast and ovarian cancer risk in Pakistan.

Risk factors for mortality in young children living under various socio-economic conditions in Lahore, Pakistan: with particular reference to inbreeding

Risk factors such as maternal age, parity, previous siblings' death, inbreeding of parents, birth weight, birth length were examined in a population-based prospective study in four population groups at different levels of urbanization in and round Lahore, Pakistan. From September 1984 to March 1995, 2967 full-term, single born infants were followed from the 5th month of gestation to 12 months of age. Logistic regression analysis showed a significant relative risk (RR) of infant death associated with parents' consanguinity (RR = 1.8), birth weight (RR = 1.8) and elder siblings' death (RR = 1.7). The risk attributed to these factors was 28, 17 and 25%, respectively. The number of lethal equivalents per gamete is about one. The B/A ratio 10.36 suggests that the genetic load is likely to be mutational. In countries like Pakistan, where consanguinity is favourably practiced, a substantial proportion of infant deaths may be prevented by cessation of such marriages. The implications of this finding for the Pakistani community are discussed.

A study of possible deleterious effects of consanguinity

The aim of the study was to determine whether consanguineous marriages result in reproductive wastage and an increased incidence of illness in the offspring in a community with a long history of inbreeding and an expected high rate of consanguineous marriage. A representative sample of 2200 women aged > or = 15 years from Dubai and Al Ain, two cities in the United Arab Emirates, representing on the one hand a modern metropolis and on the other a traditional society, were studied. A questionnaire, which included questions on age, parity, gravidity, number of stillbirths, number of abortions, number of children alive, neonatal deaths and specific illnesses in children, was administered by nurses in antenatal and gynaecological clinics in the two cities. The rate of consanguineous marriage was 50.5% and parity, gravidity, ages and number of children were similar in consanguineous and non-consanguineous groups. There was no significant difference in rates of abortion, stillbirth and neonatal death between the two groups. Overall, there was statistically significant higher reproductive wastage in consanguineous couples, but when the category of less than second cousins was excluded from the consanguineous group no difference was found in reproductive wastage between consanguineous and non-consanguineous marriages. Children born to consanguineous unions also had significantly higher incidences of illnesses (37.1%) than those of non-consanguineous unions (29%). The occurrence of malignancies, congenital abnormalities, mental retardation and physical handicap was significantly higher in offspring of consanguineous than non-consanguineous marriages. In conclusion, consanguinity did not result in reproductive wastage, but was found to be an important factor in the causation of specific illnesses in offspring.

Severe mental retardation in 2 to 24-month-old children in Lahore, Pakistan: a prospective cohort study

Severe mental retardation (developmental quotient (DQ) < 50) was investigated in 1303 children from 2 to 24 months of age, born during 1984-87 in four population groups representing different socio-economic levels in and around Lahore, Pakistan. The incidence per 1000 live births was 22 in the periurban slum, 9 in the urban slum, 7 in the village and 4 in the upper middle class group. The aetiology was prenatal in 79%, perinatal in 14% and untraceable in 7% of cases. Down's syndrome was the most common cause of severe mental retardation (36%). Impairments were studied at 2 years of age. Impairment of language was present in all, while locomotor dysfunction was seen in 89% of cases. Epilepsy and cerebral palsy were each present in 22% of cases. Mortality among these severely mentally retarded children was 36%.

An epidemiological/genetic study of mental subnormality in Assiut Governorate, Egypt

The aim of this investigation was to study the epidemiologic and genetic aspects of mental subnormality (MS) in Assiut Governorate, representing the Egyptian population. The sample comprised 3000 randomly selected subjects from three localities: one urban (Assiut City) and two adjacent rural villages. Age-matched controls were chosen for comparison. The Stanford-Binet test was administered to each individual. During history-taking special attention was paid to consanguinity and categorization on a genetic basis. The results revealed 116 cases with MS, showing an overall prevalence of 3.9%, which varied in the three locations: 3.4% in Assiut City, and 3.8% and 4.4% in the two rural locations. Clinico-genetic classification revealed the following: idiopathic MS 27.6%, MCA/MR syndromes 24.1%, primary CNS defect 12.9%, Martin-Bell syndrome 10.3%, inborn errors of metabolism 9.5%, tetratogenic and environmental causes 5.2%, MS and epilepsy 4.3%, chromosomal disorders 3.4% and MS associated with psychiatric disorder 2.6%. Parental consanguinity was found in 65% of the total sample, which emphasizes the role played by that factor in the etiology of mental subnormality in Egypt.

Early child health in Lahore, Pakistan: IX. Perinatal events

In Pakistan there are a number of acute problems related to maternal and infant health in the perinatal period. There is also lack of reliable data needed for the formulation of action strategies. To provide a database 1490 women have been followed from the 5th month of pregnancy in four different areas at various levels of urbanization and socio-economic development. After adjusting for gestational age, the proportion of newborns with weight for length < -2SDS in relation to the Swedish National Standard was 12-31% for boys and 12-25% for girls, the figure being highest in the most deprived area. Preterm birth was infrequent compared with IUGR. The overall prevalence rate of birth defects was 21% out of which 8% were severe defects. The overall perinatal mortality rate was 56/1000 births, with rates of 60, 75, 36 and 33/1000 births for the village, periurban slum, urban slum and the upper middle class. Two thirds of the deaths were related to either a continuation of intrauterine disturbances or severe congenital defects incompatible with life. One third of the deaths were due to infection; mostly diarrhoea, clinical sepsis and ARI. Neonatal mortality was significantly related to birth length (< -2SDS, odds ratio 5.5) and length of gestation (< 37 weeks, odds ratio 5.6) and was to a lesser extent related to weight (< -2SDS, odds ratio 2.0) and weight for length (< -2SDS, odds ratio 1.3). Forty percent of the mothers had weight for height below -2SDS, 23-35% had height < -2SDS. Forty percent of mothers from a subset within the cohort had a hemoglobin < 10 gm/dl and 20% showed signs of pre-eclampsia. This presentation raises the issue of expanding the current Child Survival Programs into the perinatal period as well.