Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Data discrepancies between the census and civil registration systems in Kuwait : reasons, implications and Solutions

GLMM - Gulf Labour Markets and MigrationA comparison for 1995, 2005, and 2011 reveals large discrepancies in the two main sources of population data, the censuses and the civil registration system. Possible reasons and implications of the observed discrepancies are discussed, and suggestions are made for actions and policies that might help improve data quality. This analysis suggests that the numbers recorded by the Public Authority for Civil Information (PACI) are likely to be relatively more reliable and valid than the census. However, a conclusive statement about this requires additional objective analysis. A system of post-enumeration sample surveys may be established as a usual mechanism for checking the accuracy of census data. Also, special studies designed to ensure the accuracy of PACI data should be conducted periodically.The GLMM programme is conducted by the Gulf Research Centre (GRC) and the Migration Policy Centre (MPC) and financed by the Open Society Foundations (OSF)

Second generation non-nationals in Kuwait: achievements, aspirations and plans.

About 18 per cent of all non-nationals in Kuwait were born there and have lived there at least half their life, thus comprising the second generation. A survey of 973 high school students revealed that one-third of the parents among Arabs were born in Kuwait, rendering high school students the third generation. Second generation non-nationals are typically educated, mid-level professionals and their children. They are part of extended family units residing in Kuwait. Compared with their parents, the second generation working persons (n = 252) have made considerable progress in educational level. Arabs and Asians are distinct segments of the second generation. Arabs are likely to form a larger part of the future population mix than Asians, since larger percentages of the former wish to attain higher education, and plan to look for work, in Kuwait. Socioeconomic characteristics and achievements of the second generation suggest that this group can contribute effectively to the continued advancement of Kuwait

Recent amnesty programmes for irregular migrants in Kuwait and Saudi Arabia : some successes and failures

GLMM - Gulf Labour Markets and MigrationHardly any research is available on the patterns of irregular migration in the Gulf countries, home to about 23 million migrant workers and their families. The objective of this paper is to briefly document the volume and types of irregular migration in the region and to evaluate the response of irregular migrants to recent amnesty programmes in Kuwait and Saudi Arabia for regularising their stay or facilitating their departure. Irregular migrants in Kuwait were defined as those overstaying their residence, visit, or other visa. In Saudi Arabia, they were defined as those overstaying their visa, working for someone other than their sponsor, or in an occupation that did not match their work permit. Of the 124,000 irregular migrants in Kuwait in 2011, only 37 percent departed or regularised their stay while the rest remained in the country illegally. Bangladeshis were the largest group among irregular migrants, followed by Egyptians and Indians. In Saudi Arabia in 2013, about one million irregular migrants availed the amnesty to depart while more than 4 million regularised their stay. The scale of regularisation was very large and is likely to have exerted major impact on the structure and functioning of the Saudi labour market. Some reasons for the low compliance with amnesty, especially in Kuwait, are discussed and suggestions are offered for increasing such compliance in future.The GLMM programme is conducted by the Gulf Research Centre (GRC) and the Migration Policy Centre (MPC) and financed by the Open Society Foundations (OSF)

The Role of Interspousal Communication in Adoption of Family Planning Methods: A Couple Approach

Of the several approaches designed to study the adoption of family plann¬ing methods one approach emphasizes the dynamics related to the husband-wife dyad, especially communication and interaction between the spouses as related to family planning behaviour. Interspousal communication has been shown to be an important variable in family planning behaviour in relatively underdeveloped as well as developed societies. Authors of the well-known Puerto Rican family study attributed a great deal of importance to interspousal communication as an explanatory factor in family planning and fertility behaviour [5 and 6]. Hill [6] described communi¬cation as the "hub" variable and concluded that the principal factors in family planning adoption were emphasis on planning, communication between spouses and the ability to come to a joint decision. Using data from a survey in East Pakistan (now Bangladesh), Green [3] showed that contraceptive use was correlated directly with interspousal com¬munication. Among non-user couples, 75 % of the husbands and 69 % of the wives said they had learned nothing from their spouses, compared with only 45% and 17% of user husbands and wives saying they had learned nothing from each other. Green feels that one of the major barriers to diffusion of action-associated knowledge about family planning is the lack of communication between spouses

Work Participation of Currently Married Women in Pakistan: Influence of Socio-Economic and Demographic Factors

The study of trends and structure of female labour force participation in -developing countries has attracted considerable attention over the past few years. Several international comparisons based on religious as well as socio-cultural and demographic differentials have been made. See, for example, Youssef [23, 24 and 25], Denti [6] and Boserup [4]. The primary focus of most of such studies consists of analysing female labour force participation rates and structure by controlling for one or two background factors like age or family structure. Fong's study [9] of West Malaysian women seems to be one of the few studies that have concentrated on analysing in a detailed and exhaustive manner the social and economic correlates of female work participation. Among the studies relating to labour force participation of Pakistani women, historical trends (Farooq [7]), structural set up (Farooq [8] and Bean |1 and 2]), and socio-cultural factors (Papanek [15], Pastner [16] and Saeed "[17]) have been analysed. Attempts have also been made at studying the cor¬relates of labour force participation, both for males and females [26 and 8].1 These studies have been referred to in the following sections wherever felt relevant

Pakistani labour emigration: new destinations in Europe

In the first part of this paper a historical overview is made of Pakistani labour emigration to the countries of the Persian Gulf, and to Anglo-Saxon countries in general and to the United Kingdom in particular. In the second part of the paper the new European labourmarkets which Pakistani emigrants have been increasingly discovering is analyzed. In this sense, Spain has become one of the new destinations. The author goes on to point out the specific nature of this new situation and at the same time details some of the future implications for Spain

Changes in Female Roles in Pakistan: Are the Volume and Pace Adequate? (Invited Lecture)

The question that I have set out to answer in today's presentation is a valueladen one, since I plan to give you my perception of how adequately (or inadequately) the roles of women are changing in Pakistan. My conclusions are, however, based on an objective and scientific evaluation of the existing data. With regard to data, I do not need to belabour the subject of the shortage of data or the dearth of good quality data before an audience like the present one. The shortages and weaknesses of demographic and socio-economic data are all too well known to you. I will therefore go directly to setting out the organization of my presentation. I will begin with a brief discussion of the terms of reference which have guided my analysis. This is followed by an investigation of the quantifiable changes in the roles of women. The time period covered under this section falls generally between 1951 and 1981, owing mainly to the availability of census data for these years. In the third section I will focus on the adequacy of changes in relation to national targets, as well as the international experience on the various indicators of change. In the final section, I will discuss the issues and complexities involved in bringing about changes in the existing roles and role definitions

Recent Labor Immigration Policies in the Oil-Rich Gulf: How Effective Are They Likely To Be?

[Excerpt] The oil-rich Gulf countries comprise a region with exceptionally high international migration of persons originating from a wide range of countries. The six countries that comprise this sub-region include Bahrain, Kuwait, Oman, Qatar, SaudivArabia, and United Arab Emirates (UAE), which are joined together for several purposes in an association known as the Gulf Cooperation Council (GCC). For the last three decades expatriates have come to outnumber nationals in several of the GCC countries’ populations. During the 1970s and 1980s, large scale migration of “guest” workers started as a response to the increase in the price of oil, and the consequent plans of the GCC countries for rapid development. Such plans necessitated the import of very large numbers of foreign workers since the indigenous labor forces were usually small in number and did not have the variety of skills required for the development of infrastructure and other projects. In the initial stages, construction workers were a major category of workers imported. While the demand for construction workers declined somewhat with the completion of projects, a persistent demand for such workers still exists, especially for the creation of new housing projects and buildings required for the growing number of nationals. The GCC countries have fairly high population growth rates and the number of births per woman is generally more than 4 in case of most countries. In some countries such as the UAE, construction projects are also under way as a means of investment, especially in Dubai. Besides construction workers, another major category of workers consists of those in cleaning services, helpers, and domestic service. Among domestic workers, women generally constitute a majority in most of the GCC countries. Among the sending countries, Sri Lanka, Philippines, Indonesia and India are the major ones. Over the years, the number of domestic workers has been increasing. In Kuwait, for example, housemaids comprised 7.1 % of Kuwait’s population (of 2.87 million) and numbered 203,406 in 2005 (PACI, 2005). Table 1 indicates the predominance of expatriates in Gulf countries. The percentage of non-nationals ranged from a low of 24% in Oman to 78% in Qatar in 2005. In case of the labor force, more than half in each country comprised expatriates in the early 2000s. In 2005, the combined estimated GCC population was 35.8 million with expatriates constituting 12.8 million (35.7 %). It was estimated that if the expatriate population continued to increase at the present rate it might reach 18 million after ten years. UN estimates for 2005 indicate that in the largest GCC country, Saudi Arabia, foreigners constitute 6.4 million (or 26 %) of the 24.5 million residents. Some other sources report the number of foreigners to be as high as 8.8 million. However, various estimates suggest that foreigners comprise 56-70% of the labor force and 95 % of the private sector workforce. In UAE, foreigners constitute 71 % of the 4.5 million residents (Table 1); and fill 98% of the private sector jobs. The continued predominance of foreign workers in the population and labor force of the GCC countries has been accompanied by a whole range of policies to regulate and manage such migration. A general policy aimed at curtailing the number of foreign workers has been present for several years. This general policy started getting translated into action and implementation through various means during the mid 1990s. The goal of this paper is to highlight the major policies and discuss some of the social and economic factors that may facilitate or hinder their effective implementation. An important reason for the increasingly active and forceful implementation of policies to reduce migration is the rising levels of unemployment in the GCC countries, described in the next section.pub08_12.pdf: 3541 downloads, before Oct. 1, 2020