Sequencing data of cell-free DNA fragments in living-related liver transplantation for inborn errors of metabolism

Graft derived cell-free DNA was recently reported as a non-invasive biomarker to detect graft damage or rejection after liver transplantation. There are a number of methods for quantification of Gcf-DNA,3 including quantitative-PCR, digital droplet PCR and massively parallel sequencing (next generation sequencing). Here we present the NGS4 data and fragment size distribution of cell-free DNA in the plasma of patients with inborn errors of metabolism who underwent living-related liver transplantation. For more insights please see Analysis of fragment size distribution of cell-free DNA: a potential noninvasive marker to monitor graft damage in living-related liver transplantation for inborn errors of metabolism. [1].

Living-related liver transplantation Inborn errors of metabolism more insights please see Analysis of fragment size distribution of cell-free DNA: a potential noninvasive marker to monitor graft damage in living-related liver transplantation for inborn errors of metabolism. [1]. © 2020 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data
Blood specimens from 11 patients with inborn errors of metabolism (IEM) who underwent livingrelated liver transplantation were collected at six specific time-points (d0, d1, d7, d14, d30, and d60). All the blood samples were drawn in the morning of the given days. This article shows the sequencing data and fragment size profile of cell-free DNA in the plasma of the transplant recipients. The total sequencing reads and reads aligned to Y-chromosome of each patient are summarized in Table 1. Each plasma DNA sample has generated 5.22 ± 1.02 million (mean ± SD) sequencing reads.
Analysis of the sequencing read lengths showed that cell-free DNA fragments were routinely present in the circulating plasma with a peak size around 165 base pairs (bp) before operation. Moreover, the size became shorter at post-operative day 1 and returned to a normal size when measured at day 7 or day 14. Despite this finding, there was a noticeable profile difference among participating subjects in the overall size distribution of their cfDNA (Fig. 1). We observed that cell-free DNA fragments in the plasma after liver Specifications

Value of the Data
The data indicate that cell-free DNA in the plasma after liver transplantation is composed of different groups of cell-free DNA fragments. These groups have different size ranges and Graft-derived cell-free DNA is present mainly in the shorter fragments. The data will be helpful for understanding the physical characteristics of Gcf-DNA 1 in plasma of patients with inborn errors of metabolism after liver transplantation. The data presented here will be useful for developing a cost-effective and novel non-invasive method to monitor graft injury after liver transplantation transplantation were composed of a group with a shorter fragment size (105-145bp) and another group with a longer fragment size (160-170bp) (Fig. 1). An overlap between graft-derived cell-free DNA and recipient-derived cell-free DNA was observed in the intermediate fragment size of 145e160bp. Based on the size distribution of cell-free DNA fragments, the sequencing reads were categorized into two groups (105-145bp, >145bp) ( Table 1), which were subsequently used for S/L-Frag calculation [1]. Sequencing reads from Y-chromosome in the sex-matched pairs were used for Gcf-DNA quantification [1].

Sample preparation and sequencing
Five milliliters of EDTA blood specimens were collected from 11 patients with IEMs, including Ornithine Transcarbamylase Deficiency (OTCD), Propionic Acidemia (PA), Carbamoyl Phosphate Synthetase 1 Deficiency (CPS1D), Primary Hyperoxaluria (PH), N-acetyl Glutamic-acid Synthase Deficiency (NAGSD), Ethylmalonic Encephalopathy (EE) and Methylmalonic Acidemia (MMA), at 6 specific timepoints after living-related liver transplantation (i.e. day 0, day 1, day 7, day 14, day 30 and day 60). All of the procedures and informed consent were approved by the Department of Ethics Committee at the Beijing Friendship Hospital of the Capital Medical University (Beijing, China) (approval document number: 2017-P2-080-02). All the legal guardians have provided written informed consent before living donor liver transplantation. Cell-free plasma was separated from the blood samples via two centrifugations (4 C at 2500Âg for 10 minutes and 4 C at 15,500Âg for 10 minutes). The resultant plasma was stored at À80 C until further analysis. DNA fragment from 600 mL of cell-free plasma was extracted by using Circulating Nucleic Acid Kit (Qiagen, Germany) [1]. The libraries were constructed by Ion Plus Fragment Library Kit (Life Technologies, USA) on the Ion Proton platform and then quantified using a Qubit Fluorometer. Subsequently, the selected libraries were pooled together with different barcodes and sequenced using an Ion Proton system (Life Technologies).

Sequencing data analysis
All sequencing data were aligned to the human genome reference sequences (version: NCBI Build37/hg19) using TMAP software (version 4.6.11). Unique reads whose mapping quality scores (MAPQs) were greater than 10 and whose lengths were longer than 35 bp were used in subsequent analyses [2]. In the sex-mismatched pairs, the proportion of reads from Y-chromosome (% chrY) was calculated and then used to determine the male DNA concentration in plasma.

Fragment size analysis
The reads mapped to hg19 were converted from Binary Alignment/Map (BAM) format to Browser Extensible Data (BED) format by using BEDTools software, and the length of each read was calculated by subtracting the start of the read from its end in the BED file. The size distribution of cell-free DNA in the recipient plasma was analyzed by calculating the percentage of read counts with each fragment size (ranging from 100 to 200bp) in total read counts. The sequencing reads were then grouped by their lengths, read counts of shorter fragments (105-145bp) and longer fragments (160-170bp) were used for further study on the S/L-Frag calculation in the research paper [1].