Data source of Microbial Genomics data sets

Following informed consent that was obtained from all the patients biopsy was done on each patient in a side room at the out-patient surgical clinic, using a 14-guage semi-automated spring-loaded Tru-cut Guillotine type biopsy needle made by Tsunami Medical, Italy. Each biopsy procedure was done under aseptic conditions. Local anaesthetic used was 1% xylocaine in 1:100,000 adrenaline strength.

The procedure began with the patient lying supine on the couch, the affected breast was identified, exposed and the breast lump to be biopsied located. The patient was asked to put her hand underneath her head on the ipsilateral side of the affected breast to allow for adequate exposure and prominence of the breast lump. A pre-biopsy breast examination of the concerned breast was again undertaken and the findings noted. Specific findings documented included:

breast lump location (breast quadrant) and the size of the lump. The sizes were estimated using a tape-rule.

The skin overlying the breast lesion was cleansed with 1:200 Hibitane solution followed by methylated spirit. Local infiltration was carried out with 1ml of 1%

adrenalized xylocaine (1: 100,000) using 5ml syringe with a 25-gauge needle.

36

A transverse skin crease incision of less than 0.5cm in length and 0.1cm deep using size No. 11 sterile surgical blade was made over the area of the skin overlying the lump. The Tru-cut biopsy needle spring (size 14) was then activated. This was done by drawing out the plunger which pulled-in the sharp-end of the needle close to its sheath that stopped it from further retraction inward, compressing the spring to its maximum, as it does so. The index finger and the thumb of author’s left hand were firmly applied to the lump to be biopsied. This was done for stabilisation and needle’s guidance. Following this, the activated needle was then directed at an angle of 30-degree upward to the mass or lump to prevent traumatic injury to the chest wall whenever the gun will be fired. Before firing the gun, the tip of activated needle was ensured that it abutted on the mass by applying firm pressure which pushed the needle’s tip into the lump while the author’s left hand index finger and thumb were still stabilising the lump. The gun of the biopsy needle was then fired to acquire the tissue. This was done by inserting middle and ring-fingers in the already provided two plastic rings at the base of biopsy needle and the activated plunger was then pressed upon by the thumb of the right hand.

Six tissue- cores were each taken. A sample each was obtained from the upper, middle and lower portions of the lump, on each side. This was done to ensure adequate coverage of probable areas of malignant tissue. The central area of the tumour was avoided; this was to avoid acquisition of necrotic tissue which will

37

not reveal malignant features for diagnosis. The necrosis usually stems from deprivation of oxygen and other optimum conditions necessary for cellular growth lacking in the centre of tumour. The tissue samples thus acquired were immediately immersed into the fixative (10% neutral buffered formalin) contained in a universal bottle bearing patient’s bio-data. The fixative used was freshly prepared by LUTH pathology laboratory unit which was supplied within 5-15 minutes before the commencement of biopsy procedure. The tissues were then sent to LUTH histopath-laboratory for histopathology of the specimens and determination of their receptor statuses.

The incision was dressed with firm sterile dressing materials with edges well apposed. After the procedure the patients were observed for five minutes for possible early complications like pain or haemorrhage and were given post-biopsy oral antibiotics, tablet Augmentin 625mg 12 hourly for 5-days to prevent infection and analgesics for pain, capsule tramadol 50mg twice daily for 3days.

They were instructed to wait and get their follow-up appointment during which they were equally instructed to report to the hospital without delay in case of any untoward complications if necessary, before the next clinic appointment day.

Histopathology results of the biopsy specimens and their receptor statuses were later retrieved by the author (who also participated in the receptor-status estimation process to a reasonable point; rest done by expert laboratory scientist

38

for quality results). The data were documented, collated and analysed by the author. The histological types and grades of specimen and the different modalities of treatment administered to patients were also documented by the author. The modalities included: surgery (136 patients; 66.99% in all; 70 patients had modified radical mastectomy, 66 patients had extended simple mastectomy), chemotherapy (203 patients; 100%; all had adjuvant chemotherapy, only 56 patients had neo-adjuvant chemotherapy for matted lymph nodes prior to surgery), radiotherapy (all 203 patients; 100% had radiotherapy), hormonal therapy (139 patients; 68.47% in all; while 136 patients had Tamoxifen, and 3 patients had Trastuzumab). All were documented by the author. All patients had clinical axillary node evaluation by the author and those that were both clinically palpable (192 patients) and non- clinically palpable (11 patients; equally had no axillary nodes at surgery) were fully documented prior to treatment.