LymphGen 2.0

Study Name (Optional)

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• Select Sample Annotation File [?]

Help: Sample Annotation File
Sample Annotationfile (Required):
This tab-delimited text file contains information about the data availability of the samples being analyzed. Each row indicates a sample to be analyzed. It consists of the following four required columnsin order:

Sample name: A text string used to identify the sample.
Copy number availability: a binary variable set to 1 if copy number data is available for that sample, set to 0 if copy number data is not available for that sample.
BCL2 Translocation: a binary variable set to 1 if that sample has a BCL2 translocation, set to 0 if that sample does not have a BCL2 translocation. If there is no information regarding BCL2 translocation, this should be set to "NA".
BCL6Translocation: a binary variable set to 1 if that sample has a BCL6 translocation, set to 0 if that sample does not have a BCL6 translocation. If there is no information regarding BCL6 translocation this should be set to "NA".

Download example Sample Annotation File

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Example Sample Annotation File (click to download)

• Select Mutation Gene List [?]

Help: Mutation Gene List File
Mutation Gene List file (Required):
A text file with a single column indicating the NCBI Entrez Gene IDs, for all genes that were analyzed for mutations.

Every ENTREZ.ID included in the mutation flat file should be included on this list, but this list may include genes that were not found to have alternations in any of the samples.

This list should apply to all samples run on the array. If the different samples have different gene lists (for example, if they are analyzed on differenttargeted arrays), then they should be run through the LymphGen algorithm in separate batches.

Example Mutation Gene List

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Example Mutation Gene List (click to download)

• Select Mutation Flat File [?]

Help: Mutation Flat File
Mutation Flat file (Required):
This is a tab-delimited text file with each row indicating a single alteration on a single sample.
If a sample has multiple alterations for a gene, all should be listed on separate rows. The file includes the following three required columns and a final optional column:

Sample name (Required): The sample that has the alteration. These should match the sample names given in the Sample Annotation file.
ENTREZ.ID (Required): The NCBI Entrez Gene ID number for the gene containing the alteration.
Type (Required): The type of alteration chosen from the following set of possible values:
1. TRUNC: indicating a nonsense mutation in the coding region of the gene.
2. MUTATION: indicating a missense or frameshift mutation in the coding region of the gene.
3. Synon: indicating a mutation in the 5’UTR of the gene or a synonymous mutation in the coding region within 4kb of the transcription start site.
4. L265P: indicating a L265P mutation of the MYD88 gene. (see below)
Location (Recommended): The chromosome location of the start of the mutation according to the HG37 genome build.

Special considerations:
The LymphGen predictor treats L265P mutations differently from all other mutations of MYD88; so in order for accurate prediction, mutations of the L265P locus of MYD88 should be given the Type "L265P".
Alternatively, if location is included for the MYD88 mutations, the identification of L265P will be handled automatically.
For NOTCH1 and NOTCH2 we only consider truncation mutations that affect the C-terminal PEST domain (mutation base pair position less than 139391455 for NOTCH1, and mutation base pair position less than 120459150 for NOTCH2).
For CD79B, we considered only mutations that would selectively alter their C-terminal ITAM regions. Specifically, we choose truncating mutations with mutation base pair position less than 62007172 or non-truncating mutations with mutation base pair position less than 62006800.
EZH2 mutations are restricted to those that targeted the catalytic domain (mutation base pair position between 148508764 and 148506238.

If no location information is available, we recommend including all NOTCH1, NOTCH2, EZH2 and CD79B mutations since most fall within these their respective regions. If a location columns is included, mutations in these gene outside of their prescribed regions will be automatically eliminate, as will Synon mutations outside of the 4kb range of the start site.

Example Mutation Flat File

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Example Mutation Flat File (click to download)

• Select a Copy Number Class [?]

Help: Copy Number Class
Below the data input area is a set of flags that should be used to further specify what data is available.
With the exception of the individual availability of copy number as specified in the sample annotation file, it is assumed that these flags apply to all samples in the uploaded data.
If different samples required different flags, then they should be analyzed in separate runs.

Copy number class

No copy number:
Use this flag if no copy number data is available on any samples. This selection overrides the Sample Annotation file.
Full copy number:
Use this flag if copy number data is available for some samples and is able to distinguish between single copy gains and losses vs. multiple copy amplifications and homozygous losses.
HOMDEL and AMP only:
Use this flag if the copy number platform only has the sensitivity to detect homozygous deletions or multiple copy amplifications.
HETLOSS and GAIN only:
Use this flag if the copy number platform only indicates an increase or decrease in copy number but is unable to determine the number of copies gained or lost.

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No Copy Number Full Copy Number HOMDEL and AMP only HETLOSS and GAIN only

• Select Copy Number Gene List [?]

Help: Copy Number Gene List
Copy Number Gene List file (Required if copy number is included):
A text file with a single column indicating the NCBI Entrez Gene IDs for all genes that were analyzed for copy number.
Every ENTREZ.ID included in the Mutation Flat file should be included on this list, but this list may include genes that were not found to have alternations in any of the samples. This list should apply to all samples run on the array. If the different samples have different gene lists (for example, if they are analyzed on different targeted arrays), then they should be run through the LymphGen algorithm in separate batches.

Example Copy Number Gene List

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Example Copy Number Gene List (click to download)

• Select Copy Number Flat File [?]

Help: Copy Number Flat File
Copy Number Flat file (Required if copy number is included):
This tab-delimited text file lists for each sample the genes that are overlapped by focal (30Mb or less) regions of copy-number change.
If a region overlaps multiple genes, all genes overlapped by that region should be listed on separate rows.
If a gene is covered by multiple regions of abnormal copy number on a sample, then include each on a separate row. Although not required, including copy number information will improve prediction accuracy, and its exclusion will prevent the prediction of the A53 subtype.

The file consists of the following three columns:

Sample name: The sample that has the region of copy number change. These should match the sample names given in the Sample Annotation file
ENTREZ.ID: The NCBI Entrez Gene ID number for the gene overlapped by the region.
Type: The type of the copy number change for the region chosen from the following set of possibilities.
1. Gain: Indicating a single copy increase in copy number.
2. Amp: Indicating an increase in copy number of two or more.
3. HETLOSS: indicating a heterozygous loss of a single copy.
4. HOMDEL: indicating complete loss of both alleles in the region.

Example Copy Number Flat File

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Example Copy Number Flat File (click to download)

• (Optional) Select Arm Flat file [?]

Help: Arm Flat File
Arm Flat file (Recommended if Copy number is included):
A tab-delimited text file indicating copy number changes of chromosomal arms for all samples. It is not required for the LymphGen algorithm but including this information will improve the prediction accuracy.
We define an arm as having a change in copy number if more than 80% of the length of the arm has that change or one of larger effect. So, for example, an arm that has 60% of its length covered by single copy gains and an additional 30% covered by a multiple copy amplification should be counted as having a Gain for that arm.
Whole chromosome changes are defined as those that have a given abnormality in both the p and q arms of the chromosome.

This file has the following three columns:

Sample name: The sample that has the arm with the copy change. These should match the sample names given in the Sample Annotation file.
Arm: The arm or chromosome with altered copy number. Arms are indicated by a number followed by p or q (e.g., 6p, 18q or Xp). Whole chromosomal changes are indicated by the chromosome number followed by "chrom" (e.g., 3chrom or Ychrom).
Type: The type of the copy number change for the arm chosen from the following set of possibilities
1. Gain: Indicating a single copy increase in copy number.
2. Amp: Indicating an increase in copy number of two or more.
3. HETLOSS: indicating a heterozygous loss of a single copy.
4. HOMDEL: indicating complete loss of both alleles in the region.

Example Copy Number Flat File

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Example Arm File (click to download)

• Select Subtypes [?]

Help: Subtypes Subtypes
Flag the subtypes you want to be considered for prediction.
By default, all subtypes are selected. If, due to a limited set of available features, one of the subtypes has extremely poor performance, it may be helpful to unselect a given subtype so as to not adversely affect the other predictions.
If no copy number is available, then the A53 subtype will be excluded; also, if NOTCH1 is not in the Mutation gene list, then the N1 subtype will be excluded even if the N1 flag is selected.

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BN2 EZB MCD N1 ST2 A53

• Additional Flags [?]

Help: Additional Flags Additional flags
Has L265P: Deselect this flag if you lack mutation location information and so cannot determine whether a given MYD88 mutation hits the L265P location.

Has Trunc: Deselect this flag if you lack the ability to distinguish between truncating and non-truncating mutations.

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Has MYD88 L265P Has TRUNC

Format Error!
Please review and fix the following errors with the data you provided:

LymphGen 2.0

Supply Input Files or Load Example Data Need help?