Tissue sampling of biliary tract carcinomas (BTCs) for molecular characterization is challenging. The aim of this study was to investigate the possibility of identifying individual actionable mutations derived from bile cell-free DNA (cfDNA) using targeted deep sequencing. Ten BTC patients, four with gallbladder carcinomas and six with cholangiocarcinomas, were enrolled in the present study. Using targeted deep sequencing with a panel of 150 tumor-related genes, paired bile cfDNA and tumor DNA were analyzed for mutational variants individually and then compared. The present study, to the best of our knowledge, is the first to reveal that bile cfDNA is predominantly comprised of long DNA fragments, which is not the case for plasma cfDNA. Herein, paired bile cfDNA and tumors from ten BTC patients were examined using targeted deep sequencing. When comparing bile cfDNA and tumor DNA for single nucleotide variation (SNV)/insertion and deletion (Indel), the results using targeted deep sequencing revealed high sensitivity (94.7%) and specificity (99.9%). Additionally, the sensitivity of detecting a copy number variation (CNV) was 75.0%, with a specificity of 98.9%. When comparing two bile extraction methods, including percutaneous transhepatic cholangial drainage and operation, no significant difference in SNV/Indel or CNV detection sensitivity was noted. Moreover, when examining the tumor stage and incidence site, AJCC stage II and the distal bile duct both had significantly decreased CNV detection sensitivities. The present study revealed that targeted deep sequencing can reliably detect mutational variants within bile cfDNA obtained from BTC patients. These preliminary results may shed light on bile cfDNA as a promising liquid biopsy for BTC patients.

Reprogramming of somatic cells to induced pluripotent stem cells rewrites the code of cell fate at the chromatin level. Yet, little is known about this process physically. Here, we describe a fluorescence recovery after photobleaching method to assess the dynamics of heterochromatin/euchromatin and show significant heterochromatin loosening at the initial stage of reprogramming. We identify growth arrest and DNA damage-inducible protein a (Gadd45a) as a chromatin relaxer in mouse embryonic fibroblasts, which also enhances somatic cell reprogramming efficiency. We show that residue glycine 39 (G39) in Gadd45a is essential for interacting with core histones, opening chromatin and enhancing reprogramming. We further demonstrate that Gadd45a destabilizes histone-DNA interactions and facilitates the binding of Yamanaka factors to their targets for activation. Our study provides a method to screen factors that impact on chromatin structure in live cells, and identifies Gadd45a as a chromatin relaxer.

Here, we present results of a pilot project that measured δ 13 C and δ 15 N values in bone collagen (ribs and femora) as well as dentin serial sections to examine individual dietary life histories at a Late Neolithic (4500 BP) site known as Gaoshan Ancient City (高山古 城) located on the Chengdu Plain in Sichuan Province, China. The isotopic data of the bones indicate that humans consumed C 3 -based foods, which corresponds to the dominance of rice agriculture in this region. However, the isotopic data of the dentin serial sections of five individuals display much more positive δ 13 C values than those of the bones, strongly suggesting that millets (a C 4 crop) contributed substantially to human diets during the weaning process and early childhood. Furthermore, the isotopic profiles of dentin sections of the first molars and canines demonstrate that the cession of weaning was individually variable and completed between~2.5 and 4 years of age. Although limited in scope, this pilot study offers new evidence of millet consumption during human growth and development even though individuals relied on rice exclusively as adults.Moreover, our study provides another perspective with which to rethink the role that millets played during the development and spread of millet agriculture to the south of China in terms of cultural exchange and migration. KEYWORDS carbon and nitrogen isotope analysis, Chengdu Plain, millet, serial sampling, weaning 1 | INTRODUCTION Over the last 40 years, carbon (δ 13 C) and nitrogen (δ 15 N) stable isotope ratio analysis of bulk collagen from human and animal bones has become a routine method to investigate a wide range of archaeological questions relevant to diet, evolution, mobility, social hierarchy, breastfeeding and weaning patterns, disease, nutritional stress, agriculture, and animal domestication (e.g., Britton, 2017; Lee-Thorp,

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While methods for detecting SNVs and indels in circulating tumor DNA (ctDNA) with hybridization capture-based next-generation sequencing (NGS) have been available, copy number variations (CNVs) detection is more challenging. Here, we present a method enabling CNV detection from a 150-gene panel using a very low amount of ctDNA. First, a read depth-based CNV estimation method without a paired blood sample was developed and cfDNA sequencing data from healthy people were used to build a panel of normal (PoN) model. Then, in silico and in vitro simulations were performed to define the limit of detection (LOD) for EGFR, ERBB2, and MET. Compared to the WES results of the 48 samples, the concordance rate for EGFR, ERBB2, and MET CNVs was 78%, 89.6%, and 92.4%, respectively. In another cohort profiled with the 150-gene panel from 5980 lung cancer ctDNA samples, we detected the three genes’ amplification with comparable population frequency with other cohorts. One lung adenocarcinoma patient with MET amplification detected by our method reached partial response to crizotinib. These findings show that our ctDNA CNV detection pipeline can detect CNVs with high specificity and concordance, which enables CNV calling in a non-invasive way for cancer patients when tissues are not available.