Whole Genome Amplification Methods Research Articles

Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species.

Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.

Recent advances and application in whole‐genome multiple displacement amplification

BackgroundThe extremely small amount of DNA in a cell makes it difficult to study the whole genome of single cells, so whole‐genome amplification (WGA) is necessary to increase the DNA amount and enable downstream analyses. Multiple displacement amplification (MDA) is the most widely used WGA technique.ResultsCompared with amplification methods based on PCR and other methods, MDA renders high‐quality DNA products and better genome coverage by using phi29 DNA polymerase. Moreover, recently developed advanced MDA technologies such as microreactor MDA, emulsion MDA, and micro‐channel MDA have improved amplification uniformity. Additionally, the development of other novel methods such as TruePrime WGA allows for amplification without primers.ConclusionHere, we reviewed a selection of recently developed MDA methods, their advantages over other WGA methods, and improved MDA‐based technologies, followed by a discussion of future perspectives. With the continuous development of MDA and the successive update of detection technologies, MDA will be applied in increasingly more fields and provide a solid foundation for scientific research.

Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol.

Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represents the main way to understand more deeply the pathogenesis of the neoplasm, but it is also a potential tool to understand the evolution of the tumor population with respect to its response to therapy. Pre-analytical phase for single-cell genomics analysis is crucial to obtain a cell population suitable for single-cell sorting, and whole genome amplification is required to obtain the necessary amount of DNA from a single cell in order to proceed with sequencing. Here, we evaluated the impact of different methods of cellular immunostaining, fixation and whole genome amplification on the efficiency and yield of single-cell sequencing.

Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level

Here, we report a pilot study paving the way for further single cell genomics studies in Leishmania. First, the performances of two commercially available kits for Whole Genome Amplification (WGA), PicoPLEX and RepliG were compared on small amounts of Leishmania donovani DNA, testing their ability to preserve specific genetic variations, including aneuploidy levels and SNPs. We show here that the choice of WGA method should be determined by the planned downstream genetic analysis, PicoPLEX and RepliG performing better for aneuploidy and SNP calling, respectively. This comparison allowed us to evaluate and optimize corresponding bio-informatic methods. As PicoPLEX was shown to be the preferred method for studying single cell aneuploidy, this method was applied in a second step, on single cells of L. braziliensis, which were sorted by fluorescence activated cell sorting (FACS). Even sequencing depth was achieved in 28 single cells, allowing accurate somy estimation. A dominant karyotype with three aneuploid chromosomes was observed in 25 cells, while two different minor karyotypes were observed in the other cells. Our method thus allowed the detection of aneuploidy mosaicism, and provides a solid basis which can be further refined to concur with higher-throughput single cell genomic methods.

Genome-wide capture sequencing to detect hepatitis C virus at the end of antiviral therapy

BackgroundViral relapse is a major concern in hepatitis C virus (HCV) antiviral therapy. Currently, there are no satisfactory methods to predict viral relapse, especially in the era of direct acting antivirals in which the virus often quickly becomes undetectable using PCR-based approaches that focus on a small viral region. Next-generation sequencing (NGS) provides an alternative option for viral detection in a genome-wide manner. However, owing to the overwhelming dominance of human genetic content in clinical specimens, direct detection of HCV by NGS has a low sensitivity and hence viral enrichment is required.MethodsBased on template-dependent multiple displacement amplification (tdMDA), an improved method for whole genome amplification (Wang et al., 2017. Biotechniques 63, 21–27), we evaluated two strategies to enhance the sensitivity of NGS-based HCV detection: duplex-specific nuclease (DSN)-mediated depletion of human sequences and HCV probe-based capture sequencing.ResultsIn DSN-mediated depletion, human sequences were significantly reduced in the two HCV serum samples tested, 65.3% → 55.6% → 33.7% (#4727) and 68.6% → 56% → 21% (#4970), respectively for no normalization, self- and driver-applied normalization. However, this approach was associated with a loss of HCV sequences perhaps due to its micro-homology with the human genome. In capture sequencing, HCV-mapped sequencing reads occupied 96.8% (#4727) and 22.14% (#4970) in NGS data, equivalent to 1936x and 7380x enrichment, respectively. Capture sequencing was then applied to ten serum samples collected at the end of HCV antiviral therapy. Interestingly, the number of HCV-mapped reads was significantly higher in relapsed patients (n = 5) than those from patients with sustained virological response (SVR) (n = 5), 102.4 ± 72.3 vs. 2.6 ± 0.55, p = 0.014.ConclusionsOur data provides concept evidence for a highly sensitive HCV detection by capture sequencing. The abundance difference of HCV sequencing reads at the end of HCV antiviral therapy could be applied to predict treatment outcomes.

Effectiveness of whole genome amplification prior to short tandem repeat analysis for degraded DNA

Short tandem repeat (STR) analysis is prone to failure as DNA is frequently damaged by various environmental factors; hence, increasing the number of starting templates may constitute a feasible approach to improve STR profiling success. Whole genome amplification (WGA) is often applied to bolster starting template quantity. Moreover, WGA can reportedly be used on degraded DNA samples in forensics. Therefore, we utilized a PCR-based WGA method, termed “modified improved primer extension preamplification” (mIPEP), prior to STR analysis of degraded DNA, as this method is less affected by DNA quantity and quality than most others. Saliva from four volunteers was dried on glass fiber filter papers (paper) and glass slides (glass) and irradiated with UVA light (365 nm). The mIPEP method was initiated using 5, 0.5, and 0.05 ng of DNA following DNA extraction. The DNA degradation index (DI) was calculated based on the ratio of 129 to 41 bp DNA fragments; lower numbers indicate higher degradation. Following mIPEP, STR analysis was performed using the AmpFlSTR Identifiler PCR amplification kit. The number of detectable STR loci, with and without mIPEP, decreased according to reduced DI in a different manner for the various DNA concentrations extracted from paper and glass. Specifically, for the 5 ng DNA sample on paper, at a DI < 0.2, the number of detectable STR loci was greater with mIPEP than without it, owing to fewer locus drop-outs. Similarly, the 0.05 ng DNA sample deposited on paper, at DI ≥ 0.7, exhibited higher numbers of detectable STR loci when prepared using mIPEP owing to fewer allele drop-outs. Moreover, among samples deposited on glass, the 0.05 ng DNA sample at DI ≥ 0.4 afforded a larger number of detectable STR loci when prepared using mIPEP than those without mIPEP, owing to fewer locus drop-outs. These findings suggest that performing mIPEP in accordance with sample DNA condition (e.g., quantity and quality) may lead to increased success of STR analysis. Notably, the conditions identified as most responsive to mIPEP were consistent across both UVA-irradiated and environmentally-damaged sample states. Taken together, our results suggest that applying mIPEP would be beneficial to obtain improved STR profiles under conditions involving severely degraded samples with large quantities of DNA, or with small quantities of DNA albeit with slight degradation.

Abstract 5363: A direct amplicon-based targeted sequencing assay for mutation analysis of single circulating tumor cells and correlation with circulating tumor DNA

Abstract There is increasing interest in sequence analysis of circulating tumor cells (CTCs) to identify actionable mutations that may complement circulating tumor DNA (ctDNA) findings. Because the amount of DNA present in a single cell is miniscule (~6 pg), whole genome amplification (WGA) is typically performed prior to next generation sequencing (NGS) library preparation. Existing WGA methods have inherent amplification biases leading to non-uniform genome coverage that can cause dropout of desired targets, as well as replication errors that can lead to false positive results. Targeted sequencing is an alternative approach that does not require WGA. We modified the CleanPlex® OncoZoom® Cancer Hotspot Panel protocol to perform targeted sequencing of single CTCs isolated by the RareCyte platform using A549 cell line spike-in and patient samples. We also used the CleanPlex panel to evaluate ctDNA from plasma isolated by blood collection tubes from two manufacturers (RareCyte and Streck). In both cases we compared OncoZoom results with and without prior WGA. Increased uniformity of coverage with decreased target dropout was observed when CleanPlex NGS libraries were prepared directly from cell lysates without WGA. Median read depth increased 48-fold when compared to the WGA method. On average, 23 out of 29 (79%) variants present in bulk A549 genomic DNA were observed without WGA in single model CTCs, while 15 of 29 (52%) were observed after WGA. Additionally, the false positive error frequency of non-WGA samples was 8-fold lower than in the WGA samples. CTCs and cell-free DNA from two metastatic breast cancer patients were also sequenced using OncoZoom. In one patient, PIK3CA E542K, a well-documented oncogenic mutation, was observed in 3 of 5 CTCs. In the other, ERBB2 L755S, a known HER2-reactivating mutation associated with chemoresistance, was found in 3 of 5 CTCs. Both patients' variants were present at similar allelic frequencies in plasma isolated from RareCyte and Streck cell-free DNA BCT tubes. Single-cell CleanPlex amplicon-based sequencing without prior WGA resulted in libraries with more complete and consistent coverage and lower error frequencies, enabling efficient and accurate assessment of somatic mutations in CTCs. This approach shows promise for cell-based liquid biopsy diagnostic applications. Citation Format: Nolan G. Ericson, Vidushi Kapoor, Guoying Liu, Alisa C. Clein, Daniel E. Sabath, Eric P. Kaldjian, Tad George. A direct amplicon-based targeted sequencing assay for mutation analysis of single circulating tumor cells and correlation with circulating tumor DNA [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5363.

Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet.

Whole genome amplification (WGA) is crucial for whole genome sequencing to investigate complex genomic alteration at the single-cell or even single-molecule level. Multiple displacement amplification (MDA) and multiple annealing and looping based amplification cycles (MALBAC) are two most widely applied WGA methods, which have different advantages and disadvantages, dependent on research objectives. Herein, we compared the MDA and MALBAC to provide more information on their performance in droplets and tubes. We observed that the droplet method could dramatically reduce the amplification bias and retain the high accuracy of replication than the conventional tube method. Furthermore, the droplet method exhibited higher efficiency and sensitivity for both homozygous and heterozygous single nucleotide variants (SNVs) at the low sequencing depth. In addition, we also found that MALBAC offered a greater uniformity and reproducibility and MDA showed a better efficiency of genomic coverage and SNV detection. Our results provided insights that will allow future decision making.

Utility of Plasmodium falciparum DNA from rapid diagnostic test kits for molecular analysis and whole genome amplification

BackgroundRapid diagnostic tests (RDTs) have become the most common diagnostic tool for detection of Plasmodium falciparum malaria, in particular in remote areas. RDT blood spots provide a source of parasite DNA for molecular analysis. In this study, the utility of RDTs for molecular analysis and the performance of different methods for whole genome amplification were investigated.MethodsPositive P. falciparum RDTs were collected from Kayin, Myanmar from August 2014 to January 2016. The RDT samples were stored for 6 months, 9 months, 20 months, 21 months, and 32 months before DNA extraction and subsequent molecular analysis of P. falciparum kelch 13 (pfkelch13) mutations, P. falciparum multidrug resistance 1 (pfmdr1), and P. falciparum plasmepsin 2 (pfplasmepsin2) gene amplification. In addition, performance of four whole genome amplification (WGA) kits were compared, including REPLI-g®, MALBACTM, PicoPLEX®, and GenomePlex®, for which DNA quantity and quality were compared between original DNA and post-WGA products.ResultsThe proportion of successful amplification of the different molecular markers was similar between blood spots analysed from RDTs stored for 6, 9, 20, 21, or 32 months. Successful amplification was dependent on the molecular markers fragment length (p value < 0.05): 18% for a 1245 bp fragment of pfkelch13, 71% for 364 bp of pfkelch13, 81% for 87 bp of pfmdr1, 81% for 108 bp of pfplasmepsin2. Comparison of the four WGA assay kits showed that REPLI-g®, MALBACTM, and PicoPLEX® increased the quantity of DNA 60 to 750-fold, whereas the ratio of parasite DNA amplification over human DNA was most favourable for MALBAC®. Sequencing results of pfkelch13, P. falciparum chloroquine resistance transporter (pfcrt), P. falciparum dihydrofolate reductase (pfdhfr) and six microsatellite markers assessed from the post-WGA product was the same as from the original DNA.ConclusionsBlood spots from RDTs are a good source for molecular analysis of P. falciparum, even after storage up to 32 months. WGA of RDT-derived parasite DNA reliably increase DNA quantity with sufficient quality for molecular analysis of resistance markers.

Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level

Circulating tumor cells (CTCs) have a great potential for noninvasive diagnosis and real-time monitoring of cancer. A comprehensive evaluation of four whole genome amplification (WGA)/next-generation sequencing workflows for genomic analysis of single CTCs, including PCR-based (GenomePlex and Ampli1), multiple displacement amplification (Repli-g), and hybrid PCR- and multiple displacement amplification–based [multiple annealing and loop-based amplification cycling (MALBAC)] is reported herein. To demonstrate clinical utilities, copy number variations (CNVs) in single CTCs isolated from four patients with squamous non–small-cell lung cancer were profiled. Results indicate that MALBAC and Repli-g WGA have significantly broader genomic coverage compared with GenomePlex and Ampli1. Furthermore, MALBAC coupled with low-pass whole genome sequencing has better coverage breadth, uniformity, and reproducibility and is superior to Repli-g for genome-wide CNV profiling and detecting focal oncogenic amplifications. For mutation analysis, none of the WGA methods were found to achieve sufficient sensitivity and specificity by whole exome sequencing. Finally, profiling of single CTCs from patients with non–small-cell lung cancer revealed potentially clinically relevant CNVs. In conclusion, MALBAC WGA coupled with low-pass whole genome sequencing is a robust workflow for genome-wide CNV profiling at single-cell level and has great potential to be applied in clinical investigations. Nevertheless, data suggest that none of the evaluated single-cell sequencing workflows can reach sufficient sensitivity or specificity for mutation detection required for clinical applications.

DNA 5-Methylcytosine-Specific Amplification and Sequencing.

DNA 5-methylcytosine (5mC)-specific mapping has been hampered by severe DNA degradation and the presence of 5-hydroxymethylcytosine (5hmC) using the conventional bisulfite sequencing approach. Here, we present a 5mC-specific whole-genome amplification method (5mC-WGA), with which we achieved 5mC retention during DNA amplification from limited input down to 10 pg scale with limited interference from 5hmC signals, providing DNA 5mC methylome with high reproducibility and accuracy.

Abstract P4-01-10: Targeted exome sequencing of circulating tumor cells in breast cancer

Abstract Background: Next-generation sequencing (NGS) has provided the means to comprehensively analyze somatic mutations in solid tumors. The major challenge is the accurate detection of somatic variants in low-quality DNA from formalin-fixed paraffin-embedded (FFPE) tissues and circulating tumor cells (CTCs) as white blood cells (WBCs) or other background cell populations confound variant identification. The aim of our study was to evaluate the feasibility of combining whole genome amplification (WGA) with hybridization capture-based, targeted exome sequencing in identifying clinically relevant variants in low-quality and limited input metastatic breast cancer (MBC) samples. Methods: For clinical samples, we collected 7.5 mL of blood in Streck tubes and FFPE biopsies from 5 newly diagnosed MBC patients. The CTCs were isolated with the ANGLE Parsortix using a 10um cassette within 24h of blood draw. WBCs from the same patients were profiled to eliminate germline contaminants. We used spiked cell lines (CTC mimics) as a positive control. MDA-MB-231 cells (n=50) were spiked into 7.5ml healthy donor whole-blood. We used peripheral blood not processed on the Parsortix as a negative control (no spiked cells). We performed exome sequencing on a total of 20 samples (experimental samples: spike-in MDA-MB-231 samples (S1 and S2, n=2), positive control bulk MDA-MB-231 cells (P1 and P2, n=2) and negative control WBCs (WL1 and WL2, n=2); clinical samples: CTCs (n=5), MBC (n=4) and WBCs (n=5)). We used the Repli-G WGA method and the SeqCap EZ MedExome Probes that targets the human exome for ~4600 medically relevant genes, followed by sequencing using the Illumina HiSeq2500. Somatic mutations were called with GATK MuTect2 in clinical samples and Samtools using Partek Flow for experimental samples. The variant annotation was performed using SnpEff. Results: The sequencing quality of all 6 spike-in experimental samples showed that &amp;gt;75% of the reads were overlapping in genomic features. The total number of variants identified in P1 and P2 were 69,954 and 69,848, respectively. The number of variants identified in S1 and S2 was 51,359 and 50,798 respectively. We found a substantial overlap of 67% (47,201/ 69,954) common variants in P1 and S1. Likewise, an overlap of 64% common variants (45,392/69,848) was detected in P2 and S2. We analyzed the pattern of somatic variants in both coding and noncoding regions, resulting in the identification of 8786 variants in MBC (n=4) and 638 variants in CTCs (n=5). With further filtering steps, we detected 1959 coding variants in MBC and 118 variants in CTCs. SnpEff predicted that 74% of these variants in CTCs (88/118) and 14% in MBC (274/1959) had a high impact on protein function. A total of 25 common genes were also identified in CTCs and MBC in which variants were found in protein-coding regions. We matched a list of genes having coding variants in CTCs and MBC with the actionable gene panel of a commercial genomic testing platform (FoundationOne) and a precision oncology database (OncoKB) cancer gene list. The CTCs (3/5 samples) harbored alterations in a total of 11 FoundationOne genes and 9 OncoKB genes. We identified 54 actionable genes that showed overlap with FoundationOne and 104 genes with OncoKB in all 4 MBC samples. The copy number alterations (CNAs) analysis showed a larger number of amplifications in CTCs and deletions in MBC. Conclusion: We established the feasibility of exome sequencing of medically relevant genes in detecting known and unknown variants in a breast cancer cell line spike in experiment. This workflow has further been validated on CTCs and MBC samples by sequencing both low-input material and low-quality FFPE samples. This approach has a high potential for the identification of the complete repertoire of mutations along with CNAs and for monitoring the presence of actionable alterations throughout the course of treatment. Citation Format: Pushpinder K. Bains, Daniel Campo, Tania B. Porras, Janice Lu, Julie E. Lang. Targeted exome sequencing of circulating tumor cells in breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-01-10.

Assessment of two whole genome amplification techniques in terms of soil community profiles

Whole genome amplification (WGA) facilitates the metagenomics study of low biomass environments, with the risks of introducing biases and community skewing. The objective of this study was therefore to compare two common WGA methods in terms of community distortion. Multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) were evaluated with three contrasting soils and by 16S rRNA genes amplicon and whole genome shotgun sequencing. Both WGA technologies yielded stable amplification from nanogram quantities of soil DNA. The MiSeq sequencing of 16S rRNA genes demonstrated considerable loss of species richness and highly skewed community profiles for MDA-derived templates compared to the actual communities. Bacillales of low GC genome were consistently enriched in all MDA libraries. In contrast, MALBAC captured the community differences between the three soils as revealed by a hierarchical clustering analysis, and the community distortion was moderate in terms of bacterial richness. Unlike MDA, MALBAC may enrich bacteria of high GC genomes. Prokaryotic community analysis of the shotgun data confirmed the findings obtained by the 16S rRNA amplicon sequencing. Despite the wide use of MDA, these findings implicate MALBAC as promising in characterizing microbial communities in low biomass soils and highlights the potential of community profile as a quality control for WGA of environmental samples.

Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples

Whole genome sequencing (WGS) is a widely available, inexpensive means of providing a wealth of information about an organism's diversity and evolution. However, WGS for many pathogenic bacteria remain limited because they are difficult, slow and/or dangerous to culture. To avoid culturing, metagenomic sequencing can be performed directly on samples, but the sequencing effort required to characterize low frequency organisms can be expensive. Recently developed methods for selective whole genome amplification (SWGA) can enrich target DNA to provide efficient sequencing. We amplified Coxiella burnetii (a bacterial select agent and human/livestock pathogen) from 3 three environmental samples that were overwhelmed with host DNA. The 68- to 147-fold enrichment of the bacterial sequences provided enough genome coverage for SNP analyses and phylogenetic placement. SWGA is a valuable tool for the study of difficult-to-culture organisms and has the potential to facilitate high-throughput population characterizations as well as targeted epidemiological or forensic investigations.

Centrifugal-Driven Droplet Generation Method with Minimal Waste for Single-Cell Whole Genome Amplification.

High-quality whole-genome amplification (WGA) of individual cells is the primary step for characterizing the genetic information on single cells in biology and medicine. As the most popular single-cell WGA method, multiple displacement amplification (MDA) is often plagued by the nonuniform amplification. The droplet MDA has been an innovative tool to solve this dilemma by mitigating the amplification bias and increasing the genomic coverage. Despite these advantages, the time-consuming droplet generation process, the waste of small volume samples and the difficulty of parallel operation for multiple single-cell samples remain major obstacles. Herein, we introduce a centrifugal-driven droplet generation method for rapid and convenient generation of uniform droplets from a relatively small volume sample (5 μL) in 60s with more than 98% sample utilization. We have performed quantitative digital droplet PCR using this method, demonstrating its capability of amplifying nucleic acids at the single-molecule level. Single-cell centrifugal-driven droplet MDA (cd-MDA) has also been conducted for single-cell sequencing, achieving uniform amplification and broad genomic coverage. With the single-molecule sensitivity, minimum sample waste, high genomic coverage, and excellent sequencing evenness, this centrifugal-driven droplet generation method is promising for convenient and scalable use in digital PCR and single-cell whole-genome research.

Diseases Have No Borders, Neither Should Research!

In response to recent anti-Chinese sentiment in the US, Sunney Xie uses his own experiences to assert that American ideals should not be replaced by nationalism and populism and that everybody wins in Sino-US scientific collaborations, contrary to what Americans are led to believe: that China is the sole beneficiary.

7. GENETIC TESTING FOR COPY NUMBER VARIATIONS IN FIRST POLAR BODIES AND OOCYTES BY SINGLE-CELL NEXT-GENERATION SEQUENCING

Introduction Female meiotic errors are the main cause of whole chromosomal aneuploidy in human embryos and significantly contribute to early embryo loss. Meiotic chromosomal malsegregation occurs during divisions of the maturing oocyte in oogenesis concurrently with extrusion of two polar bodies: polar body first (PB1) and polar body second (PB2). Based on meiosis mechanism, genome of a single oocyte can be deduced by analyzing its sibling polar bodies. PB genetic testing can identify abnormalities of maternal meiotic origin and may be the only form of preimplantation genetic testing for aneuploidies (PGT-A) accepted by patients who object embryo biopsy for ideological reasons. In the majority of previous studies, array comparative genomic hybridization (aCGH) was a method of choice for comprehensive chromosome testing in polar bodies. Here, we test the use of single-cell next-generation sequencing (NGS) method in polar body testing for detecting copy number variations (CNVs) in PB1 genome and validate methods for whole genome amplification (WGA) of PB1. Material and methods In this study, single-cell NGS technology was used to asses ploidy status of oocytes and their sibling PB1. A total of 120 single cells (60 first polar bodies and 60 oocytes) were collected from in vitro fertilization (IVF) couples and subjected for WGA using four different kits based on three distinct amplification systems: (i) polymerase chain reaction (PCR-based WGA), (ii) multiple displacement amplification (MDA) or (iii) multiple annealing and looping-based amplification cycles (MALBAC). WGA products were processed and analyzed with VeriSeq PGS MiSeq kit on MiSeq sequencing platform (Illumina) and random samples were validated with the aCGH method. Amplification uniformity and accuracy for CNV detection of the four tested kits were evaluated. Results Ploidy status was determined for 112 of 120 (93,3%) samples (84/112 based on direct analysis and 28/112 based on indirect analysis of the well-amplified sibling PB1 or oocyte). Estimated aneuploidy rate for the studied group which resembles the total oocyte abnormality resulting from meiosis I errors rate was 33% (37/112 samples). In the group of well-amplified PB1-oocyte pairs (33/60) a 97% concordance between the chromosomal status of PB1 and the corresponding oocyte was observed. Both whole chromosome nondisjunction (6 of 37 aneuploid samples) and abnormal chromatid pre-division and segregation were detected (31 of 37 aneuploid samples). The result is concordant with previous studies - abnormal chromatid segregation was the dominant aneuploidy-causing mechanism. Differences in WGA kits performance including amplification uniformity, aneuploidy calling potential and a number of interpretable NGS results were evaluated and the most optimal kit for PB1 genome WGA was pre-selected. Results from aCGH validation of the randomly selected samples showed full consistency with the NGS results. Conclusions The NGS-based method used for PB1 genome analysis showed a high predictive potential of PB1 in deducing ploidy status of the corresponding oocyte and is a promising method for PGT-A of oocytes. The study also contributes to a better understanding of the chromosome segregation patterns and maternal meiosis errors. Supported by: POIR.02.03.02-14- 0092/17

Abstract 439: Targeted single cell DNA sequencing without prior whole genome amplification for mutational analysis of circulating tumor cells

Abstract Background. RareCyte has developed platform technology for visual identification and single cell retrieval of rare cells in blood, including circulating tumor cells (CTCs). There is increasing interest in mutational analysis of circulating tumor cells (CTCs) as a liquid biopsy application. Because of the minuscule amount of DNA present in a single cell (~6 pg), whole genome amplification (WGA) is typically performed prior to next generation sequencing (NGS) library preparation. Existing WGA methods have inherent amplification biases leading to non-uniform genome coverage that can cause dropout of desired targets, as well as elevated error rates that can lead to false positive mutations. Amplicon-based next generation sequencing (abNGS) is a high-throughput method which enables genetic confirmation of malignancy and discovery of de novo pathogenic mutations. Here we present a method for performance of single cell abNGS on model CTCs without prior WGA using a commercially available pan-cancer hotspot panel. Methods. A549 lung cancer cells as model CTCs (mCTCs) were spiked into whole blood, which was processed by AccuCyte® separation onto slides. After formalin fixation, multi-parameter immunofluorescence and automated imaging (CyteFinder®) were used to identify CTCs - visualized as nucleated cells expressing epithelial markers (cytokeratin or EpCAM) and not expressing white blood cell markers. mCTCs were mechanically retrieved by CytePicker® into PCR tubes and either amplified by WGA (PicoPLEX®) or lysed in a PCR-compatible lysis buffer. WGA products or cell lysates were used as template for the AmpliSeq™ Cancer HotSpot Panel v2 for Illumina® library preparation; additional PCR cycles were added during target amplification to compensate for low DNA input in the non-WGA samples. Libraries were sequenced on an Illumina MiSeq and analyzed using the BaseSpace bioinformatics suite. Results. Single mCTCs that underwent amplicon-based NGS library prep direct from cell lysate (non-WGA) displayed increased uniformity of coverage with decreased target dropout when compared to WGA cells. Median read depth increased 7-fold with the non-WGA method. On average, 8 of 15 variants present in bulk A549 genomic DNA were observed in single mCTCs sequenced after WGA, while 12 out of 15 were observed with the non-WGA method. Additionally, the false positive error frequency of non-WGA samples was &amp;lt; 5% of the WGA samples. The non-WGA method was applied to CTCs identified in blood from a prostate cancer patient and confirmed presence of PTEN and TP53 mutations identified by cell-free DNA analysis. Conclusions. Amplicon-based targeted single-cell sequencing without prior WGA resulted in libraries with more complete and consistent coverage and lower error frequencies, enabling efficient and accurate assessment of somatic mutations in CTCs. Citation Format: Nolan G. Ericson, Arturo B. Ramirez, Alisa C. Clein, Celestia S. Higano, Daniel E. Sabath, Eric P. Kaldjian. Targeted single cell DNA sequencing without prior whole genome amplification for mutational analysis of circulating tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 439.

The comparison of two whole genome amplification methods: A new method of pre-implantation genetic testing (PGT-M) for Southeast Asian deletion in alpha-thalassemia using high resolution melting analysis

Introduction In Southeast Asia, alpha-thalassemia with Southeast Asian (SEA) deletion type is the most common mutations of alpha-thalassemia-1 which can cause severe form known as Bart's hydrops fetalis. For couples which carrier of single gene defects, pre-implantation genetic testing for monogenic (PGT-M) plays a role in genetic testing for selecting of unaffected embryos prior implantation. Recently, high resolution melting (HRM) analysis is a simple, rapid and widely used for genotyping and gene scanning of genetic variation. In this study, we developed HRM analysis method for detection of SEA deletion in alpha-thalassemia and compared two WGA methods, SurePlex DNA Amplification System and REPLI-g Single Cell on the performance of HRM analysis and linkage analysis. Material and Methods Retrospective study was carried out in a single private fertility clinic from 2015 to 2017. The single cell embryos were biopsied on blastocyst stage from couples with disease- carrier of SEA deletion type. The trophectoderm biopsied cells were amplified by two whole genome amplification (WGA), SurePlex DNA Amplification System-PCR based method (Illumina, USA) and REPLI-g MDA Single Cell (QIAGEN, Germany). All WGA products were analyzed with two primer pairs of HRM analysis for detection of SEA deletion type in alpha-thalassemia disease and confirmed with the informative short tandem repeated (STRs) linkage analysis. Results A total of 53 single cell biopsied were amplified with SurePlex-WGA (n=33) and REPLI-g MDA (n=20) which used as template for HRM analysis. The HRM results revealed clearly distinguished between wild type and mutant type of SEA deletion mutation in alpha-thalassemia. Comparing between two WGA methods, the HRM amplification results efficiency and allele drop out (ADO) rate of REPLI- g MDA were 95% (19/20) and 31.57% (6/19), respectively. Meanwhile, for SurePlex-WGA showed 75.76% (25/33) and 28% (7/25), respectively. Furthermore, the HRM melting profile results of REPLI-g MDA showed higher concordance rate with the informative STRs linkage analysis results (63.16%, 12/18) than that of SurePlex-WGA (48%, 12/25). Conclusions HRM analysis is an alternative technique with high sensitivity and accuracy for detecting of alpha-thalassemia mutations. The REPLI-g MDA Single Cell method with HRM analysis is suitable for detection of alpha-thalassemia1 SEA type deletion in PGT-M and provided a good concordance with informative STRs linkage analysis. However, ADO from PCR amplification could be occurred and caused of misdiagnosis which might be affected to the interpretation results of the embryos disease- status. Thus, the mutation analysis method using HRM analysis combined with STRs linkage analysis are recommend in PGT-M to avoid the effected of ADO and increase the accuracy and reliable of the PGT-M results.

Non-invasive preimplantation genetic testing for aneuploidy (NI PGT-A)

Since the initial report by Stigliani et al. (2013) about the presence of mitochondrial and nuclear DNA in human embryo culture medium, spent media (SM) has been extensively explored with the ultimate aim to develop non-invasive genetic testing (NI PGT) methods. Even after the first clinical application of NI PGT-A by Xu and colleagues (2016) using SM, the efficacy of the method for clinical utility remains under much debate as there are conflicting reports on its success rates as well concerns about non- embryonic DNA contamination. There are two key aspects determining the success of an NI PGT assay; 1) embryology parameters of culture conditions and 2) molecular methods used for downstream processing of SM samples. Most of the studies on NI PGT thus far have used SM samples derived from a single IVF centre and hence differences in choice of culture media, culture volumes, type of culture (fresh vs vitrified-thawed), and timing of sampling (Day3-Day5/6 or Day4-Day5/6) would have, in part, contributed to the differences in success rates obtained by different groups ( Shamonki et al., 2016 , Xu et al., 2016 , Feichtinger et al., 2017 , Lane et al., 2017 , Kuznyetsov et al., 2017 ). Hence, it is pertinent to develop a robust and versatile NI PGT method, functional under multiple embryo culture parameters. The choice of whole genome amplification (WGA) method is another major factor which might impact the success of NI PGT assay. As the embryonic DNA in spent media is most likely fragmented in nature, shorter DNA template lengths can pose challenge to chemistries of certain WGA methods ( Wang et al., 2004 ). Secondly, certain components of embryo culture media might impede the function of buffer and/or enzyme of the WGA system, thereby resulting in suboptimal or no amplification. We have tested two commercially available WGA methods on SM samples namely Sureplex and MDA in addition to a modified MDA approach (suitable for fragmented DNA) and found that the DNA amplification rates were significantly higher in the samples amplified with the modified MDA compared to those amplified by Sureplex and MDA methods. The origin of DNA present in SM can be a confounding factor for NI PGT assay. Microbial contamination has been reported to occur at Kastrop et al., 2007 ). More recently, Vera-Rodriguez et al. (2018) reported very high levels of maternal DNA contamination with only ∼8% of DNA fraction in the SM beingembryonic in origin. However with appropriate culture conditions and amplification methods, several other groups ( Xu et al., 2016 , Kuznyetsov et al., 2017 , Lane et al., 2017 ), including ours, have obtaineda high sex chromosomes as well as overall ploidy concordance rates (range: 72% - 95%) between SM and corresponding TE biopsies. Thisindicatesthat any potential contamination present in these samples was minimal and did not impede the end results; thereby highlighting the importance of adequate embryology culture practice as well appropriate downstream processing steps for a successful NI PGT-A assay. While a few NI PGT-A clinical trials have been initiated over the last two years, many crucial questions regarding the broader clinical efficacy of the method still remain to be answered. Nonetheless, it seems that we are one step closer to the dream of a completely non-invasive method for genetic testing of preimplantation embryos than before.