Patient info

The Patient info screen can be accessed through the patient icon on the Samples overview screen. The icon is coloured blue or red, depending on whether patient info has been completed or not, respectively. Alternatively, when opening a sample, the patient info screen can be accessed through the Patient tab on top of the page.

Open

On the Patient info screen, the following information is displayed, of which some fields can be completed or edited:

Sample

• Sample name: This field allows to edit the automatically assigned sample name

• Type: Based on the number of variants in the VCF, Moon indicates whether the VCF originates from WES/WGS data and gives an indication of the number of variants in the file. Clicking the number of SNVs redirects you to the Quality page for that sample.

• Priority: By default, all samples have standard priority. This can be changed to ‘Urgent’. After clicking the Run analysis button, analysis of Urgent samples will start as soon as the analysis of the currently running analysis is finished, or as soon as the other urgent samples in the queue have been analysed. For both standard and urgent cases, WES cases have priority over WGS cases.

• Report language: By default, automated report notes will be generated in English. However, it is also possible to select Dutch as language for the report note.

Patient

• Gender: The proband’s gender can be indicated as being male, female or unknown via the dropdown menu. The automatically predicted gender by Moon, based on the uploaded VCF file, is shown next to the selection menu, thereby lowering the risk of entering an incorrect gender.

• Age of onset of symptoms: In this field, the age of onset at which the first symptoms became apparent should be provided in years. For congenital onset of symptoms or prenatal manifestations, an age of onset of “0” can be indicated. If the exact age of onset of symptoms is unknown, the following options can be considered: approximate the age of onset based on whether the symptoms were early- or late-onset (>30 years); use the current age of the patient as age of onset; set a default age of onset of “100” if no information is available.

• Consanguinity: This box can be checked in case of known positive consanguinity in the family.

• Referral note: This field allows you to enter any information of relevance for the sample in plain text format. HPOs are automatically recognised and highlighted in (English) text, taking into account whether symptoms are present (green) or absent (red) in the patient. Clicking the ‘Add HPOs from notes’ button allows to easily fetch the HPOs highlighted in green in the text, and add these as input HPOs. Finally, this referral note will also displayed in the automatically generated PDF report, if using the Moon reporting functionality.

Open

• Symptoms (HPO): Symptoms can be provided as terms from the Human Phenotype Ontology (HPO), synonyms of HPO terms or with their Human Phenotype ID. Only terms within HPO branch ‘Phenotypic abnormality’ are supported as input. HPO terms or synonyms are auto-completed based on the entered text. See the article on HPO input for recommendations on entering HPO terms. At least one HPO term is required in order to take advantage of Moon's automated analysis pipeline. If no HPO terms are entered, the genetic data will be annotated and presented in the Filter view for manual filtering.

• Suggested symptoms: Based on the entered HPO terms and on the structure of the ontology, Moon suggests additional terms to refine the input phenotype of your patient. Simply click Add to include any of these suggested terms in the analysis. Although only 10 additional HPO terms are suggested for inclusion, more can be found through the Human phenotype ontology browser.

Family

Family relations can be defined by adding the samples of interest, healthy/affected status and relation to the proband.