Publications

There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern American ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.

Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) has a heterogeneous clinical presentation and disease course. Establishing prognosis for these patients is challenging. Identifying the factors that predict mortality in patients with RA-ILD could help guide management. A detailed systematic review was conducted in order to identify individual variables that predict mortality in RA-ILD. A literature review was performed using keywords and medical subject headings to identify all articles relating to the prognosis of RA-ILD. Studies were included if they identified predictors of mortality in adults with RA-ILD, were published in English, and included at least 10 patients with RA-ILD. Two authors independently reviewed each citation and extracted data from all studies meeting inclusion criteria. Any differences were then resolved by consensus. A total of 10 studies met our inclusion criteria. All were observational cohort studies of variable quality. Mean age of reported patients ranged from 55 to 69 years, and 41.7% of all patients were male. Median survival ranged from 3.2 to 8.1 years. Significant predictors of mortality on multivariate analysis were older age, male gender, lower diffusion capacity for carbon monoxide, extent of fibrosis, and the presence of usual interstitial pneumonia pattern. Mortality in RA-ILD is associated with several patient- and ILD-specific variables; however, previous studies are of low quality.

The lymphotoxin (LT)-pathway is a unique constituent branch of the Tumor Necrosis Superfamily (TNFSF). Use of LT is a critical mechanism by which fetal innate lymphoid cells regulate lymphoid organogenesis. Within recent years, adult innate lymphoid cells have been discovered to utilize this same pathway to regulate IL-22 and IL-23 production for host defense. Notably, genetic studies have linked polymorphisms in the genes encoding LTα to several phenotypes contributing to metabolic syndrome. The role of the LT-pathway may lay the foundation for a bridge between host immune response, microbiota, and metabolic syndrome. The contribution of the LT-pathway to innate lymphoid cell function and metabolic syndrome will be visited in this review.

BACKGROUND

Dyspnea is a hallmark symptom of idiopathic pulmonary fibrosis (IPF), and dyspnea induced physical activity limitation is a prominent driver of quality of life impairment among IPF patients.

METHODS

We examined response data for the 21 physical activity items (the first 21 of 24) from the University of California San Diego Shortness of Breath Questionnaire (UCSD) collected at baseline in a recently conducted IPF trial. We used Rasch analysis and hypothesis testing with conventional statistical methodology to achieve three objectives: 1) to examine the items to identify the one characteristic that distinguishes one from another; 2) to asses these items for their ability to measure dyspnea severity in IPF; 3) to use the items to develop a dyspnea ruler.

RESULTS

The sample comprised 178 subjects. The 21 items fit the Rasch model. There was very strong correlation between Rasch item severity and their metabolic equivalents (METS) values (r = -0.86, p < 0.0001). With the sample stratified on scores from the 21 items, there were significant between group differences in FVC%, DLCO% and distance walked during the six-minute walk test. The dyspnea ruler can be used to put dyspnea levels in a more easily understood clinical context.

CONCLUSIONS

The first 21 items from the UCSD compose a unidimensional dyspnea-with-activity scale and are both sensibly ordered and distinguished from each other by their METS values. These 21 items can be used confidently to formulate clinically-relevant inferences about IPF patients and should be considered for use as a meaningful endpoint in IPF research.