Gene expression of variant alleles.

<p>Variant allele fractions (VAFs) of each point mutation were determined from mRNA-sequencing data and compared to those from combined whole genome sequencing (WGS) and validation sequencing data. Gene variants shared in the primary and metastases (shared mutations, black), metastases but not primaries (metastases specific, blue), or only in one metastasis (private, red) in patients A1 (A) and A7 (B) are shown.</p

Clonality analysis of each tumor from patient A1.

<p>VAFs among the primary and matched metastases in patient A1 (A) and a representative evolutionary tree (B) colored by subclone based on the clonality plots in panel A, with the width of the branch indicating the approximate percentage of that clone within the tumor. Clone 1 is established in the primary tumor and seeded all distant metastases. Clones 2 and 4 from the primary tumor seeded the liver and the adrenal gland, with clone 7 concurrently seeding the liver from the primary tumor. Clones 3 and 5 from the primary tumor seeded the lung, with clone 3 also seeding the spine. Private clones include clone 6, specific to the adrenal metastasis; clone 8, specific to the primary tumor; and clone 9, specific to the spinal metastasis.</p

Molecular relatedness of matched primary and metastases.

<p>(A) Hierarchical clustering of patient A1 and A7’s tumors with 1,100 TCGA Primary samples and 98 normal breast samples analyzed using a breast cancer intrinsic gene list. The color bars under the dendrogram indicate (i) where A1 (red) and A7 (blue) specimens are clustered and (ii) the PAM50 subtype of each sample (basal-like, red; HER2-enriched, pink; luminal A, dark blue; luminal B, light blue; and normal-like, green). (B) The position of A1 (red) and the position of A7 (blue) within the basal-like cluster are highlighted. (C) The relationship of the primary and metastases for each patient based upon gene expression patterns.</p

Clinical history and distribution of metastases from patients A1 and A7, who both had clinically triple-negative and basal-like breast cancer.

<p>Clinical history and distribution of metastases from patients A1 and A7, who both had clinically triple-negative and basal-like breast cancer.</p

Oxytricha trifallax macronuclear IDBA assembly

Contigs in gzipped fasta format

Oxytricha trifallax macronuclear PCAP 2.1.8 assembly

Oxytricha trifallax macronuclear PCAP 2.1.8 assembl

Oxytricha trifallax macronuclear genome fosmids

Oxytricha trifallax macronuclear genome fosmid

Schematic of rare (MAF<1%) non-synonymous variants used in the gene-level test HDL-C in gene <i>CETP</i>.

<p>The x-axis scale (AA) is in amino acid positions. Numbers in parenthesis are the number of copies of the rare variant in persons with phenotype data. The mean HDL-C level in persons possessing variants with bold naming is increased relative to persons without the variant, for all other variants the mean HDL-C level in persons possessing variant alleles is decreased relative to persons without the variant.</p

Oxytricha trifallax macronuclear PE-Assembler/SSAKE assembly

Contigs in gzipped fasta format

Rare and common variants contribute to the association signal to HDL-C in gene <i>CETP</i>.

1<p>P-values for rs3764261 and rs5880 may be different from those recorded in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004147#pgen-1004147-t002" target="_blank">Table 2</a> because of the addition of rs2303790 and rs5883 to the model. MAC: minor allele count.</p